+++ /dev/null
-package compbio.data.msa;\r
-\r
-import java.net.ConnectException;\r
-import java.util.Set;\r
-\r
-import javax.xml.ws.WebServiceException;\r
-\r
-import org.testng.Assert;\r
-import org.testng.annotations.BeforeTest;\r
-import org.testng.annotations.Test;\r
-\r
-import compbio.metadata.AllTestSuit;\r
-import compbio.ws.client.Jws2Client;\r
-import compbio.ws.client.Services;\r
-import compbio.ws.client.WSTesterTester;\r
-\r
-public class CategoryTester {\r
-\r
- // test category membership from string constants\r
- RegistryWS registry = null;\r
-\r
- @BeforeTest(groups = AllTestSuit.test_group_webservices)\r
- public void setupTest() {\r
- try {\r
- /*\r
- * registry = Jws2Client .connectToRegistry(\r
- * "http://webserv1.cluster.lifesci.dundee.ac.uk:8089/jaba");\r
- */\r
- registry = Jws2Client.connectToRegistry(WSTesterTester.SERVER);\r
-\r
- } catch (ConnectException e) {\r
- e.printStackTrace();\r
- Assert.fail(e.getMessage());\r
- } catch (WebServiceException e) {\r
- e.printStackTrace();\r
- Assert.fail(e.getMessage());\r
- }\r
-\r
- }\r
-\r
- /*\r
- * This test will FAIL unless a connection to a running JABAWS web server is\r
- * made!\r
- */\r
- @Test(groups = AllTestSuit.test_group_webservices)\r
- public void categoryTest() {\r
- Set<Category> servicecategories = registry.getServiceCategories();\r
-\r
- boolean found = false;\r
- for (Category svccategory : servicecategories) {\r
-\r
- Set<Services> catservices;\r
-\r
- for (String category : new String[]{Category.CATEGORY_ALIGNMENT,\r
- Category.CATEGORY_CONSERVATION, Category.CATEGORY_DISORDER}) {\r
- if (category.equals(svccategory.name)) {\r
- found = true;\r
- catservices = svccategory.getServices();\r
- System.out.println("Found " + catservices.size()\r
- + " services in category " + category\r
- + "(service category string " + svccategory + ")");\r
- }\r
- }\r
- }\r
- if (!found) {\r
- Assert.fail("Could not match any category to one of the given category constants");\r
- }\r
- }\r
-\r
-}\r
+++ /dev/null
-/* Copyright (c) 2009 Peter Troshin\r
- * \r
- * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0 \r
- * \r
- * This library is free software; you can redistribute it and/or modify it under the terms of the\r
- * Apache License version 2 as published by the Apache Software Foundation\r
- * \r
- * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
- * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
- * License for more details.\r
- * \r
- * A copy of the license is in apache_license.txt. It is also available here:\r
- * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
- * \r
- * Any republication or derived work distributed in source code form\r
- * must include this copyright and license notice.\r
- */\r
-\r
-package compbio.data.sequence;\r
-\r
-import static org.testng.AssertJUnit.assertEquals;\r
-import static org.testng.AssertJUnit.assertNotNull;\r
-import static org.testng.AssertJUnit.assertTrue;\r
-import static org.testng.AssertJUnit.fail;\r
-\r
-import java.io.FileInputStream;\r
-import java.io.FileNotFoundException;\r
-import java.io.FileWriter;\r
-import java.io.IOException;\r
-import java.io.Writer;\r
-\r
-import org.testng.annotations.Test;\r
-\r
-import compbio.metadata.AllTestSuit;\r
-\r
-public class ClustalAlignmentUtilTester {\r
-\r
- @Test()\r
- public void testReadClustalFile() {\r
- try {\r
- readWriteClustal("TO1381.aln");\r
- } catch (FileNotFoundException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- } catch (Exception e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- }\r
- }\r
-\r
- static void readWriteClustal(String fname) throws IOException,\r
- UnknownFileFormatException {\r
- FileInputStream fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH\r
- + fname);\r
- Alignment seqAl = ClustalAlignmentUtil.readClustalFile(fio);\r
- assertTrue(seqAl != null);\r
- assertTrue(seqAl.getSize() == 3);\r
- assertNotNull(seqAl.getSequences());\r
- assertEquals(3, seqAl.getSequences().size());\r
-\r
- // Now try to write the alignment read\r
- Writer os = new FileWriter(AllTestSuit.TEST_DATA_PATH + fname\r
- + ".written");\r
- ClustalAlignmentUtil.writeClustalAlignment(os, seqAl);\r
- fio.close();\r
- os.close();\r
-\r
- fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH + fname\r
- + ".written");\r
- Alignment readseqs = ClustalAlignmentUtil.readClustalFile(fio);\r
- assertTrue(readseqs != null);\r
- assertTrue(readseqs.getSize() == 3);\r
- fio.close();\r
- }\r
-\r
- @Test()\r
- public void testReadClustalFileShortNames() {\r
- try {\r
- readWriteClustal("TO1381s.aln");\r
- } catch (FileNotFoundException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- } catch (Exception e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- }\r
- }\r
-\r
- @Test()\r
- public void testReadClustalFileLongNames() {\r
- try {\r
- readWriteClustal("TO1381L.aln");\r
- } catch (FileNotFoundException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- } catch (Exception e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- }\r
- }\r
-\r
-}\r
+++ /dev/null
-/* Copyright (c) 2009 Peter Troshin\r
- * \r
- * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0 \r
- * \r
- * This library is free software; you can redistribute it and/or modify it under the terms of the\r
- * Apache License version 2 as published by the Apache Software Foundation\r
- * \r
- * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
- * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
- * License for more details.\r
- * \r
- * A copy of the license is in apache_license.txt. It is also available here:\r
- * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
- * \r
- * Any republication or derived work distributed in source code form\r
- * must include this copyright and license notice.\r
- */\r
-\r
-package compbio.data.sequence;\r
-\r
-import java.io.IOException;\r
-import java.util.List;\r
-\r
-import compbio.util.FileUtil;\r
-\r
-public class FastaGeneratorManager {\r
-\r
- public static void main(String[] args) throws IOException {\r
- FastaSequenceGenerator fgen = new FastaSequenceGenerator(\r
- FastaSequenceGenerator.SeqType.PROTEIN, 50);\r
-\r
- List<FastaSequence> fslist = fgen.generateFasta(400);\r
- writeToFile(fslist, "SmallProtein.fasta");\r
-\r
- fgen = new FastaSequenceGenerator(\r
- FastaSequenceGenerator.SeqType.PROTEIN, 200);\r
-\r
- fslist = fgen.generateFasta(500);\r
- writeToFile(fslist, "200x500Protein.fasta");\r
-\r
- fgen = new FastaSequenceGenerator(FastaSequenceGenerator.SeqType.DNA,\r
- 1000);\r
- fslist = fgen.generateFasta(3000);\r
- writeToFile(fslist, "1000x3000Dna.fasta");\r
-\r
- fgen = new FastaSequenceGenerator(FastaSequenceGenerator.SeqType.DNA,\r
- 50000);\r
- fslist = fgen.generateFasta(300);\r
- writeToFile(fslist, "50000x300Dna.fasta");\r
- System.out.println("Done");\r
- }\r
-\r
- static void writeToFile(List<FastaSequence> fastalist, String filepath)\r
- throws IOException {\r
- StringBuilder sb = new StringBuilder();\r
- for (FastaSequence fs : fastalist) {\r
- sb.append(fs.getOnelineFasta() + "\n");\r
- }\r
- FileUtil.writeToFile(sb.toString(), filepath);\r
- }\r
-}\r
+++ /dev/null
-package compbio.data.sequence;\r
-\r
-import java.io.FileInputStream;\r
-import java.io.FileNotFoundException;\r
-import java.io.IOException;\r
-import java.util.ArrayList;\r
-import java.util.List;\r
-\r
-import org.testng.Assert;\r
-import org.testng.annotations.Test;\r
-\r
-import compbio.metadata.AllTestSuit;\r
-\r
-public class FastaReaderTester {\r
-\r
- static FastaSequence s0 = new FastaSequence(\r
- "zedpshvyzg",\r
- "GCQDKNNIAELNEIMGTTRSPSDWQHMKGASPRAEIGLTGKKDSWWRHCCSKEFNKTPPPIHPDMKRWGWMWNRENFEKFLIDNFLNPPCPRLMLTKGTWWRHEDLCHEIFWSTLRWLCLGNQSFSAMIWGHLCECHRMIWWESNEHMFWLKFRRALKKMNSNGPCMGPDNREWMITNRMGKEFCGPAFAGDCQSCWRKCHKTNKICFNEKKGTPTKIDHEQKDIMDILKDIDNHRNWKQCQLWLLTSKSTDQESTTMLTWSTWRDFFIIIKQPFDHKCRGALDANGDFQIAAELKWPAPMIILRQNQKTMHDKSCHHFFTNRCPLMHTTRANDKQCSWHTRKQFICQQDFTTWQHRPDTHRILPSWCMSTRRKNHIKNTPALAFSTCEMGDLPNGWAPGTIILQRQFTQAIKLPQETTGWPRCDPKFDHWNMSKWLRQLLGRDDEMIPPQCD");\r
-\r
- static FastaSequence s1 = new FastaSequence(\r
- "xovkactesa",\r
- "CPLSKWWNRRAFLSHTANHWMILMTWEGPHDGESKMRIAMMKWSPCKPTMSHFRCGLDAWAEPIRQIACESTFRM"\r
- + "FCTTPRPIHKLTEMWGHMNGWTGAFCRQLECEWMMPPRHPHPCTSTFNNNKKRLIGQIPNEGKQLFINFQKPQHG"\r
- + "FSESDIWIWKDNPTAWHEGLTIAGIGDGQHCWNWMPMPWSGAPTSNALIEFWTWLGMIGTRCKTQGMWWDAMNHH"\r
- + "DQFELSANAHIAAHHMEKKMILKPDDRNLGDDTWMPPGKIWMRMFAKNTNACWPEGCRDDNEEDDCGTHNLHRMC");\r
- static FastaSequence s2 = new FastaSequence(\r
- "ntazzewyvv",\r
- "CGCKIF D D NMKDNNRHG TDIKKHGFMH IRHPE KRDDC FDNHCIMPKHRRWGLWD"\r
- + "EASINM AQQWRSLPPSRIMKLNG HGCDCMHSHMEAD DTKQSGIKGTFWNG HDAQWLCRWG"\r
- + "EFITEA WWGRWGAITFFHAH ENKNEIQECSDQNLKE SRTTCEIID TCHLFTRHLDGW"\r
- + " RCEKCQANATHMTW ACTKSCAEQW FCAKELMMN "\r
- + "W KQMGWRCKIFRKLFRDNCWID FELPWWPICFCCKGLSTKSHSAHDGDQCRRW WPDCARDWLGPGIRGEF "\r
- + "FCTHICQQLQRNFWCGCFRWNIEKRMFEIFDDNMAAHWKKCMHFKFLIRIHRHGPITMKMTWCRSGCCFGKTRRLPDSSFISAFLDPKHHRDGSGMMMWSSEMRSCAIPDPQQAWNQGKWIGQIKDWNICFAWPIRENQQCWATPHEMPSGFHFILEKWDALAHPHMHIRQKKCWAWAFLSLMSSTHSDMATFQWAIPGHNIWSNWDNIICGWPRI");\r
- static FastaSequence s3 = new FastaSequence(" 12 d t y wi k jbke ",\r
- " KLSHHDCD" + " N" + " H" + " HSKCTEPHCGNSHQML\n\rHRDP"\r
- + " CCDQCQSWEAENWCASMRKAILF");\r
- static FastaSequence s4 = new FastaSequence(" 12 d t>y wi->foo k jbke ",\r
- " KLSHHDCD" + " N" + " H" + " HSKCTEPHCGNSHQML\n\rHRDP"\r
- + " CCDQCQSWEAENWCASMRKAILF");\r
- @Test()\r
- public void test() {\r
-\r
- List<FastaSequence> old_seqs = null;\r
- final List<FastaSequence> list = new ArrayList<FastaSequence>();\r
- try {\r
- old_seqs = SequenceUtil.readFasta(new FileInputStream(\r
- AllTestSuit.TEST_DATA_PATH + "complicated.fasta"));\r
- final FastaReader fr = new FastaReader(AllTestSuit.TEST_DATA_PATH\r
- + "complicated.fasta");\r
-\r
- while (fr.hasNext()) {\r
- final FastaSequence fs = fr.next();\r
- list.add(fs);\r
- }\r
- } catch (final FileNotFoundException e) {\r
- e.printStackTrace();\r
- Assert.fail(e.getLocalizedMessage());\r
- } catch (final IOException e) {\r
- e.printStackTrace();\r
- Assert.fail(e.getLocalizedMessage());\r
- }\r
- System.out.println("OLD: " + old_seqs);\r
- System.out.println("NEW: " + list);\r
- Assert.assertEquals(old_seqs.size(), list.size());\r
- Assert.assertEquals(old_seqs.get(0), list.get(0));\r
- Assert.assertEquals(old_seqs.get(1), list.get(1));\r
- // Assert.assertEquals(old_seqs.get(2), list.get(2));\r
- // Assert.assertEquals(seqs.get(3), list.get(3));\r
-\r
- Assert.assertEquals(FastaReaderTester.s0, list.get(0));\r
- Assert.assertEquals(FastaReaderTester.s1, list.get(1));\r
- Assert.assertEquals(FastaReaderTester.s2, list.get(2));\r
- Assert.assertEquals(FastaReaderTester.s3, list.get(3));\r
- Assert.assertEquals(FastaReaderTester.s4, list.get(4));\r
-\r
- }\r
-}\r
+++ /dev/null
-/* Copyright (c) 2009 Peter Troshin\r
- * \r
- * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0 \r
- * \r
- * This library is free software; you can redistribute it and/or modify it under the terms of the\r
- * Apache License version 2 as published by the Apache Software Foundation\r
- * \r
- * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
- * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
- * License for more details.\r
- * \r
- * A copy of the license is in apache_license.txt. It is also available here:\r
- * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
- * \r
- * Any republication or derived work distributed in source code form\r
- * must include this copyright and license notice.\r
- */\r
-\r
-package compbio.data.sequence;\r
-\r
-import java.util.ArrayList;\r
-import java.util.List;\r
-import java.util.Random;\r
-\r
-public class FastaSequenceGenerator {\r
-\r
- enum SeqType {\r
- DNA, PROTEIN\r
- }\r
-\r
- enum ProteinAlphabet {\r
- A, R, N, D, C, E, Q, G, H, I, L, K, M, F, P, S, T, W, V\r
- };\r
-\r
- enum DNAAlphabet {\r
- C, T, G, A, U\r
- };\r
-\r
- enum Letters {\r
- q, w, e, r, t, y, u, i, o, p, a, s, d, f, g, h, j, k, l, z, x, c, v, b, n, m\r
- };\r
-\r
- final SeqType seqtype;\r
- final int seqNumber;\r
- final Random rand;\r
-\r
- /**\r
- * \r
- * @param type\r
- * of the sequence to be generated one of DNA or PROTEIN\r
- * @param seqNumber\r
- * number of sequences to be generated\r
- */\r
- public FastaSequenceGenerator(SeqType type, int seqNumber) {\r
- this.seqtype = type;\r
- this.seqNumber = seqNumber;\r
- this.rand = new Random();\r
- }\r
-\r
- /**\r
- * Generate a list of Fasta formatted sequences with sequence length between\r
- * 0.5 to 1 of maxLenght. Name of the sequence as well as the sequence is\r
- * generated randomly\r
- * \r
- * @param maxSeqLength\r
- * maximum length of generated sequence\r
- * @return\r
- */\r
- public List<FastaSequence> generateFasta(int maxSeqLength) {\r
- List<FastaSequence> fastal = new ArrayList<FastaSequence>();\r
- FastaSequence seq = null;\r
- for (int i = 0; i < seqNumber; i++) {\r
- switch (this.seqtype) {\r
- case DNA:\r
- seq = new FastaSequence(generateName(), generateDna(\r
- maxSeqLength, getRandomNumber(0.5, 0.99)));\r
- break;\r
- case PROTEIN:\r
- seq = new FastaSequence(generateName(), generateProtein(\r
- maxSeqLength, getRandomNumber(0.5, 0.99)));\r
- break;\r
- default:\r
- throw new AssertionError("Cannot recognise a type!");\r
- }\r
- fastal.add(seq);\r
- }\r
- return fastal;\r
- }\r
-\r
- private String generateName() {\r
- Letters[] letters = Letters.values();\r
- int max = letters.length - 1;\r
- StringBuilder sb = new StringBuilder();\r
- for (int i = 0; i < 10; i++) {\r
- sb.append(letters[getRandomNumber(0, max)]);\r
- }\r
- return sb.toString();\r
- }\r
-\r
- private String generateProtein(int length, double variability) {\r
- ProteinAlphabet[] proteinA = ProteinAlphabet.values();\r
- int max = proteinA.length - 1;\r
- StringBuilder sb = new StringBuilder();\r
- for (int i = 0; i < length * variability; i++) {\r
- sb.append(proteinA[getRandomNumber(max)]);\r
- }\r
- return sb.toString();\r
- }\r
-\r
- private String generateDna(int length, double variability) {\r
- if (variability == 0) {\r
- variability = 1;\r
- }\r
- DNAAlphabet[] dnaA = DNAAlphabet.values();\r
- int max = dnaA.length - 1;\r
- StringBuilder sb = new StringBuilder();\r
- for (int i = 0; i < length * variability; i++) {\r
- sb.append(dnaA[getRandomNumber(max)]);\r
- }\r
- return sb.toString();\r
- }\r
-\r
- /*\r
- * Returns random integers in range from 0 to max\r
- * \r
- * @param max\r
- * \r
- * @return\r
- */\r
- private int getRandomNumber(int max) {\r
- return rand.nextInt(max);\r
- }\r
-\r
- /*\r
- * Returns random integers with value in range from min to max\r
- * \r
- * @param min\r
- * \r
- * @param max\r
- * \r
- * @return\r
- */\r
- private int getRandomNumber(int min, int max) {\r
- return new Long(Math.round((max - min) * rand.nextDouble() + min))\r
- .intValue();\r
- }\r
-\r
- private double getRandomNumber(double min, double max) {\r
- return (max - min) * rand.nextDouble() + min;\r
- }\r
-}\r
+++ /dev/null
-/* Copyright (c) 2009 Peter Troshin\r
- * \r
- * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0 \r
- * \r
- * This library is free software; you can redistribute it and/or modify it under the terms of the\r
- * Apache License version 2 as published by the Apache Software Foundation\r
- * \r
- * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
- * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
- * License for more details.\r
- * \r
- * A copy of the license is in apache_license.txt. It is also available here:\r
- * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
- * \r
- * Any republication or derived work distributed in source code form\r
- * must include this copyright and license notice.\r
- */\r
-\r
-package compbio.data.sequence;\r
-\r
-import static org.testng.AssertJUnit.assertEquals;\r
-import static org.testng.AssertJUnit.assertTrue;\r
-\r
-import java.util.List;\r
-\r
-import org.testng.annotations.Test;\r
-\r
-public class FastaSequenceGeneratorTester {\r
-\r
- @Test()\r
- public void testProteinSequenceGeneration() {\r
- FastaSequenceGenerator fs = new FastaSequenceGenerator(\r
- FastaSequenceGenerator.SeqType.PROTEIN, 100);\r
- assertEquals(100, fs.generateFasta(100).size());\r
-\r
- fs = new FastaSequenceGenerator(FastaSequenceGenerator.SeqType.DNA, 50);\r
- List<FastaSequence> flist = fs.generateFasta(100);\r
- assertEquals(50, flist.size());\r
- for (FastaSequence s : flist) {\r
- assertTrue(s.getLength() >= 50);\r
- }\r
-\r
- }\r
-}\r
+++ /dev/null
-/* Copyright (c) 2009 Peter Troshin\r
- * \r
- * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0 \r
- * \r
- * This library is free software; you can redistribute it and/or modify it under the terms of the\r
- * Apache License version 2 as published by the Apache Software Foundation\r
- * \r
- * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
- * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
- * License for more details.\r
- * \r
- * A copy of the license is in apache_license.txt. It is also available here:\r
- * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
- * \r
- * Any republication or derived work distributed in source code form\r
- * must include this copyright and license notice.\r
- */\r
-\r
-package compbio.data.sequence;\r
-\r
-import static org.testng.AssertJUnit.assertEquals;\r
-\r
-import org.testng.annotations.Test;\r
-\r
-public class FastaSequenceTester {\r
-\r
- @Test()\r
- public void testGetFormattedFasta() {\r
- FastaSequence fs = new FastaSequence(\r
- "test",\r
- "kjashf asjkdfhjkahsdfkadf fewyweyrfhjajfasdjkfkjhasdjkfaskhdfjhasdjkf "\r
- + "hdflhdghuetirwhglhasdghfjkhdfs gdsfkjghsdjfgjhdsfglkhskdjfgjhjsdkfgkhsdjkfghsdkjfgh "\r
- + "sdfjglkjhsdflkjg sdfgklhsdkfgdfkjghjkshgdflsdfgjkshdfghksdjfgkjhsdfgjkh");\r
- assertEquals(219, fs.getSequence().length());\r
- assertEquals(11, fs.getFormatedSequence(20).split("\n").length);\r
- assertEquals(3, fs.getFormatedSequence(80).split("\n").length);\r
- fs = new FastaSequence("test", "kjashf f ");\r
- assertEquals(1, fs.getFormatedSequence(80).split("\n").length);\r
- assertEquals(7, fs.getFormatedSequence(1).split("\n").length);\r
- }\r
-}\r
+++ /dev/null
-/* Copyright (c) 2009 Peter Troshin\r
- * Copyright (c) 2013 Alexander Sherstnev\r
- * \r
- * JAva Bioinformatics Analysis Web Services (JABAWS) \r
- * @version: 2.5\r
- * \r
- * This library is free software; you can redistribute it and/or modify it under \r
- * the terms of the Apache License version 2 as published\r
- * by the Apache Software Foundation This library is distributed in the hope\r
- * that it will be useful, but WITHOUT ANY WARRANTY; without even the implied\r
- * warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * Apache License for more details. A copy of the license is in\r
- * apache_license.txt. It is also available here:\r
- * \r
- * @see: http://www.apache.org/licenses/LICENSE-2.0.txt \r
- * \r
- * Any republication or derived work distributed in source code form must include \r
- * this copyright and license notice.\r
- */\r
-package compbio.data.sequence;\r
-\r
-import static org.testng.AssertJUnit.assertEquals;\r
-import static org.testng.AssertJUnit.assertFalse;\r
-import static org.testng.AssertJUnit.assertNotNull;\r
-import static org.testng.AssertJUnit.assertTrue;\r
-import static org.testng.AssertJUnit.fail;\r
-\r
-import java.io.File;\r
-import java.io.FileInputStream;\r
-import java.io.FileNotFoundException;\r
-import java.io.FileOutputStream;\r
-import java.io.IOException;\r
-import java.io.InputStream;\r
-import java.io.PrintWriter;\r
-import java.util.HashMap;\r
-import java.util.HashSet;\r
-import java.util.List;\r
-import java.util.Map;\r
-import java.util.Set;\r
-\r
-import org.testng.annotations.Test;\r
-\r
-import compbio.metadata.AllTestSuit;\r
-\r
-public class SequenceUtilTester {\r
-\r
- @Test()\r
- public void isNonAmbNucleotideSequence() {\r
- String dnaseq = "atgatTGACGCTGCTGatgtcgtgagtgga";\r
- assertTrue(SequenceUtil.isNonAmbNucleotideSequence(dnaseq));\r
- String dirtyDnaseq = "atgAGTggt\taGGTgc\ncgcACTgc gACtcgcGAt cgA ";\r
- assertTrue(SequenceUtil.isNonAmbNucleotideSequence(dirtyDnaseq));\r
- String nonDna = "atgfctgatgcatgcatgatgctga";\r
- assertFalse(SequenceUtil.isNonAmbNucleotideSequence(nonDna));\r
-\r
- nonDna = "atgc1tgatgcatgcatgatgctga";\r
- assertFalse(SequenceUtil.isNonAmbNucleotideSequence(nonDna));\r
-\r
- nonDna = "ARLGRVRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQL";\r
- assertFalse(SequenceUtil.isNonAmbNucleotideSequence(nonDna));\r
- // String ambDna = "AGTCRYMKSWHBVDN"; // see IUPAC Nucleotide Code\r
- assertFalse(SequenceUtil.isNonAmbNucleotideSequence(nonDna));\r
- }\r
-\r
- @Test()\r
- public void CleanSequence() {\r
- String dirtySeq = "atgAGTggt\taGGTgc\ncgcAC\rTgc gACtcgcGAt cgA ";\r
- assertEquals("atgAGTggtaGGTgccgcACTgcgACtcgcGAtcgA".toUpperCase(),SequenceUtil.cleanSequence(dirtySeq));\r
- }\r
-\r
- @Test()\r
- public void DeepCleanSequence() {\r
- String dirtySeq = "a!t?g.A;GTggt\ta12GGTgc\ncgc23AC\rTgc gAC<>.,?!|\\|/t@cg-c¬GA=_+(0){]}[:£$&^*\"t cgA ";\r
- assertEquals("atgAGTggtaGGTgccgcACTgcgACtcgcGAtcgA".toUpperCase(),SequenceUtil.deepCleanSequence(dirtySeq));\r
- }\r
-\r
- @Test()\r
- public void isProteinSequence() {\r
- String dirtySeq = "atgAGTggt\taGGTgc\ncgcAC\rTgc gACtcgcGAt cgA ";\r
- assertFalse(SequenceUtil.isProteinSequence(dirtySeq));\r
- String notaSeq = "atgc1tgatgcatgcatgatgctga";\r
- assertFalse(SequenceUtil.isProteinSequence(notaSeq));\r
- String AAseq = "ARLGRVRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQL";\r
- assertTrue(SequenceUtil.isProteinSequence(AAseq));\r
- AAseq += "XU";\r
- assertFalse(SequenceUtil.isProteinSequence(AAseq));\r
-\r
- }\r
-\r
- @Test()\r
- public void CleanProteinSequence() {\r
- String dirtySeq = "atgAGTggt\taGGTgc\ncgcAC\rTgc gACtcgcGAt cgA ";\r
- assertFalse(SequenceUtil.isProteinSequence(dirtySeq));\r
- // This will still be NON protein sequence despite having only correct\r
- // letters because the letters match perfectly the nucleotide sequence!\r
- assertFalse(SequenceUtil.isProteinSequence(SequenceUtil.cleanProteinSequence(dirtySeq)));\r
-\r
- String notaSeq = "atgc1tgatgcatgcatgatgmctga";\r
- assertFalse(SequenceUtil.isProteinSequence(notaSeq));\r
- assertTrue(SequenceUtil.isProteinSequence(SequenceUtil.cleanProteinSequence(notaSeq)));\r
-\r
- String AAseq = "ARLGRVRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQL";\r
- assertTrue(SequenceUtil.isProteinSequence(AAseq));\r
- assertTrue(SequenceUtil.isProteinSequence(SequenceUtil.cleanProteinSequence(AAseq)));\r
- AAseq += "XU";\r
-\r
- assertFalse(SequenceUtil.isProteinSequence(AAseq));\r
- assertTrue(SequenceUtil.isProteinSequence(SequenceUtil.cleanProteinSequence(AAseq)));\r
- }\r
-\r
- @Test()\r
- public void ReadWriteFasta() {\r
- try {\r
- FileInputStream fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH + "TO1381.fasta");\r
- assertNotNull(fio);\r
- List<FastaSequence> fseqs = SequenceUtil.readFasta(fio);\r
- assertNotNull(fseqs);\r
- assertEquals(3, fseqs.size());\r
- assertEquals(3, fseqs.size());\r
- fio.close();\r
- FileOutputStream fou = new FileOutputStream(AllTestSuit.TEST_DATA_PATH + "TO1381.fasta.written");\r
- SequenceUtil.writeFasta(fou, fseqs);\r
- fou.close();\r
- FileOutputStream fou20 = new FileOutputStream(AllTestSuit.TEST_DATA_PATH + "TO1381.fasta20.written");\r
- SequenceUtil.writeFasta(fou20, fseqs, 21);\r
- fou20.close();\r
- } catch (FileNotFoundException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (IOException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- }\r
- }\r
-\r
- // Potential Bug :- Sequence names are shortened to 2-3 letters\r
- @Test\r
- public void testReadFastaWriteClustal() {\r
- \r
- try {\r
- FileInputStream fio = new FileInputStream(\r
- AllTestSuit.TEST_DATA_PATH + "TO1381.fasta");\r
- assertNotNull(fio);\r
- List<FastaSequence> fseqs = SequenceUtil.readFasta(fio);\r
- assertNotNull(fseqs);\r
- fio.close();\r
- \r
- char gapChar = '-';\r
- FileOutputStream fou = new FileOutputStream(\r
- AllTestSuit.TEST_DATA_PATH + "TO1381.aln.written");\r
- SequenceUtil.writeClustal(fou, fseqs, gapChar);\r
- fou.close();\r
- \r
- } catch (FileNotFoundException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (IOException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- }\r
- }\r
-\r
- /**\r
- * This test tests the loading of horizontally formatted Jronn output file\r
- */\r
- @Test\r
- public void LoadJronnFile() {\r
-\r
- FileInputStream fio;\r
- try {\r
- fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH + "jronn.out");\r
- Map<String, Score> aseqs = SequenceUtil.readJRonn(fio);\r
- assertNotNull(aseqs);\r
- assertEquals(aseqs.size(), 3);\r
- Score aseq = aseqs.get("Foobar");\r
- assertNotNull(aseq);\r
- assertNotNull(aseq.getScores());\r
- assertEquals(aseq.getScores().size(), aseq.getScores().size());\r
- fio.close();\r
- } catch (FileNotFoundException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (IOException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (UnknownFileFormatException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- }\r
- }\r
-\r
- enum Trial {\r
- one, two, three\r
- };\r
-\r
- /**\r
- * This test tests the loading of horizontally formatted Jronn output file\r
- * \r
- * First seq\r
- * \r
- * M 0.86010 0.88512 0.37094\r
- * \r
- * T 0.79983 0.85864 0.44331\r
- * \r
- */\r
- @SuppressWarnings("unchecked")\r
- @Test\r
- public void ReadDisemblResults() {\r
- Map<String, Map<String,Set<Range>>> _ranges=new HashMap<String, Map<String,Set<Range>>>();\r
- Map<String, Set<Range>> ranges=new HashMap<String,Set<Range>>();\r
- Map<String,Map<String, Float>> _values=new HashMap<String, Map<String,Float>>();\r
- Map<String, Float> values = new HashMap<String, Float>();\r
- Set<Range> rset;\r
- rset = new HashSet<Range>();\r
- for (String[] se:new String[][] { { "34","41"},{"50","58"},{"83","91"},{"118","127"},{" 160","169"},{" 191","220"},{" 243","252"},{" 287","343"},{" 350","391"},{" 429","485"},{" 497","506"},{"539","547"}}) {\r
- rset.add(new Range(se));\r
- }\r
- ranges.put(DisemblResult.COILS.toString(), rset);\r
- values.put(DisemblResult.COILS.toString(), Float.valueOf(0.86010f));\r
- rset = new HashSet<Range>();\r
- for (String[] se:new String[][] { { "355","368"}}) {\r
- rset.add(new Range(se));\r
- }\r
- ranges.put(DisemblResult.REM465.toString(), rset);\r
- values.put(DisemblResult.REM465.toString(), Float.valueOf(0.88512f));\r
- rset = new HashSet<Range>();\r
- for (String[] se:new String[][] { { "190","204"}}) {\r
- rset.add(new Range(se));\r
- }\r
- ranges.put(DisemblResult.HOTLOOPS.toString(), rset);\r
- values.put(DisemblResult.HOTLOOPS.toString(), Float.valueOf(0.37094f));\r
- _ranges.put("Foobar_dundeefriends", ranges);\r
- _values.put("Foobar_dundeefriends", values);\r
- FileInputStream fio;\r
- try {\r
- fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH + "disembl.out");\r
- Map<String, Set<Score>> aseqs = SequenceUtil.readDisembl(fio);\r
- assertNotNull(aseqs);\r
- assertEquals(aseqs.size(), 3);\r
- ScoreManager sman = ScoreManager.newInstance(aseqs);\r
-\r
- for (String fs : aseqs.keySet()) {\r
- assertTrue(" Foobar_dundeefriends Foobar dundeefriends ".contains(fs));\r
- Set<Score> scores = aseqs.get(fs);\r
- assertEquals(scores.size(), 3);\r
- for (Score sc:scores) {\r
- if (_ranges.containsKey(fs)) {\r
- assertEquals("Checking range for Method "+sc.getMethod(),_ranges.get(fs).get(sc.getMethod()), sc.getRanges());\r
- assertEquals("Checking first value for Method "+sc.getMethod(), _values.get(fs).get(sc.getMethod()), sc.getScores().get(0));\r
- }\r
- }\r
- }\r
- fio.close();\r
- } catch (FileNotFoundException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (IOException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (UnknownFileFormatException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- }\r
- }\r
-\r
- /**\r
- * This method tests the loading of horizontally formatted Jronn output file\r
- * \r
- * First sequence:\r
- * \r
- * >Foobar_dundeefriends\r
- * \r
- * # GlobDoms 2-358, 373-568\r
- * \r
- * # Disorder 1-5, 206-218, 243-250, 288-300, 313-324, 359-372, 475-481\r
- * \r
- * # RESIDUE DYDX RAW SMOOTHED\r
- * \r
- * M 0.0044 -0.2259 -0.2259\r
- * \r
- * T -0.1308 -0.2170 -0.2170\r
- * \r
- * ............\r
- * \r
- * > Second sequence\r
- */\r
- @SuppressWarnings("unchecked")\r
- @Test\r
- public void ReadGlobPlotResults() {\r
-\r
- FileInputStream fio;\r
- try {\r
- fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH + "globplot.out");\r
- HashMap<String, Set<Score>> aseqs = SequenceUtil.readGlobPlot(fio);\r
- assertNotNull(aseqs);\r
- assertEquals(aseqs.size(), 3);\r
-\r
- String fsdf = null;\r
- Set<Score> scores = null;\r
- for (String fs : aseqs.keySet()) {\r
- if ("Foobar_dundeefriends".contains(fs)) {\r
- fsdf = fs;\r
- scores = aseqs.get(fs);\r
- }\r
- assertEquals(scores.size(), 5);\r
- }\r
-\r
- ScoreManager sm = ScoreManager.newInstanceSingleSequence(scores);\r
- sm.writeOut(new PrintWriter(System.out, true));\r
-\r
- for (Score score : scores) {\r
- if (score.getMethod().equals(GlobProtResult.Disorder.toString())) {\r
- assertEquals(score.getRanges().size(), 7);\r
- assertTrue(score.getScores().isEmpty());\r
- }\r
- if (GlobProtResult.valueOf(score.getMethod()) == GlobProtResult.Dydx) {\r
- assertFalse(score.getScores().isEmpty());\r
- assertTrue(score.getRanges().isEmpty());\r
- }\r
- }\r
- fio.close();\r
- } catch (FileNotFoundException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (IOException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (UnknownFileFormatException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- }\r
- }\r
-\r
- @Test\r
- public void ReadIUPredForShortAndLongDisorder() {\r
- try {\r
- Map<String, Score> scores = SequenceUtil.readIUPred(new File(AllTestSuit.TEST_DATA_PATH, "out.long"));\r
- ScoreManager man = ScoreManager.newInstanceSingleScore(scores);\r
- assertNotNull(scores);\r
- assertEquals(3, scores.size());\r
-\r
- Score score = scores.get("Foobar_dundeefriends");\r
- assertNotNull(score);\r
- assertEquals(0, score.getRanges().size());\r
- assertEquals(568, score.getScores().size());\r
- assertEquals("Long", score.getMethod());\r
-\r
- score = scores.get("Foobar");\r
- assertNotNull(score);\r
- assertEquals(0, score.getRanges().size());\r
- assertEquals(481, score.getScores().size());\r
- assertEquals("Long", score.getMethod());\r
-\r
- score = scores.get("dundeefriends");\r
- assertNotNull(score);\r
- assertEquals(0, score.getRanges().size());\r
- assertEquals(513, score.getScores().size());\r
- assertEquals("Long", score.getMethod());\r
- } catch (IOException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (UnknownFileFormatException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- }\r
- }\r
-\r
- @Test\r
- public void ReadIUPredForGlobDomain() {\r
- try {\r
- Map<String, Score> scores = SequenceUtil.readIUPred(new File(AllTestSuit.TEST_DATA_PATH, "output.glob"));\r
- assertNotNull(scores);\r
- assertEquals(2, scores.size());\r
- ScoreManager man = ScoreManager.newInstanceSingleScore(scores);\r
- assertEquals(2, man.getNumberOfSeq());\r
- Score score = scores.get("P53_HUMA");\r
- assertNotNull(score);\r
- assertEquals(2, score.getRanges().size());\r
- assertEquals(0, score.getScores().size());\r
- assertEquals("Glob", score.getMethod());\r
- score = scores.get("Foobar_dundeefriends");\r
- assertEquals(0, score.getRanges().size());\r
- } catch (IOException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (UnknownFileFormatException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- }\r
- }\r
-\r
- @Test\r
- public void ReadAAConResults() {\r
- try {\r
- InputStream inStream = new FileInputStream(AllTestSuit.TEST_DATA_PATH + "aacon_results.txt");\r
- HashSet<Score> result = SequenceUtil.readAAConResults(inStream);\r
- inStream.close();\r
- assertNotNull(result);\r
- assertEquals(result.size(), 18);\r
-\r
- inStream = new FileInputStream(AllTestSuit.TEST_DATA_PATH + "aacon_result_single.out");\r
- result = SequenceUtil.readAAConResults(inStream);\r
- inStream.close();\r
- assertNotNull(result);\r
- assertEquals(result.size(), 1);\r
- assertEquals(result.iterator().next().getScores().size(), 568);\r
- } catch (IOException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- }\r
- }\r
- @Test\r
- public void ReadJpredResults() {\r
- try {\r
- InputStream inStream = new FileInputStream(AllTestSuit.TEST_DATA_PATH + "Jpred.test1.out");\r
- List<FastaSequence> result = SequenceUtil.readJpredFile(inStream);\r
- inStream.close();\r
- assertNotNull(result);\r
- assertEquals(result.size(), 19);\r
- } catch (IOException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- }\r
- }\r
-}\r
-\r
+++ /dev/null
-/* Copyright (c) 2009 Peter Troshin\r
- * \r
- * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0 \r
- * \r
- * This library is free software; you can redistribute it and/or modify it under the terms of the\r
- * Apache License version 2 as published by the Apache Software Foundation\r
- * \r
- * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
- * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
- * License for more details.\r
- * \r
- * A copy of the license is in apache_license.txt. It is also available here:\r
- * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
- * \r
- * Any republication or derived work distributed in source code form\r
- * must include this copyright and license notice.\r
- */\r
-\r
-package compbio.engine;\r
-\r
-import static org.testng.Assert.fail;\r
-\r
-import org.testng.annotations.Test;\r
-\r
-import compbio.engine.client.ConfiguredExecutable;\r
-import compbio.metadata.JobSubmissionException;\r
-import compbio.runner.msa.ClustalW;\r
-\r
-public class EngineConfiguratorTester {\r
-\r
- @Test\r
- public void testGetAsyncEngine() {\r
-\r
- ClustalW clustal = new ClustalW();\r
-\r
- try {\r
- SyncExecutor sEngine = Configurator.getSyncEngine(Configurator\r
- .configureExecutable(clustal));\r
- } catch (JobSubmissionException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- }\r
- }\r
-\r
- @Test\r
- public void testGetSyncEngine() {\r
- ClustalW clustal = new ClustalW();\r
- try {\r
- ConfiguredExecutable<ClustalW> confClust = Configurator\r
- .configureExecutable(clustal);\r
- AsyncExecutor aEngine = Configurator.getAsyncEngine(confClust);\r
- } catch (JobSubmissionException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- }\r
- }\r
-\r
-}\r
+++ /dev/null
-/* Copyright (c) 2009 Peter Troshin\r
- * \r
- * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0 \r
- * \r
- * This library is free software; you can redistribute it and/or modify it under the terms of the\r
- * Apache License version 2 as published by the Apache Software Foundation\r
- * \r
- * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
- * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
- * License for more details.\r
- * \r
- * A copy of the license is in apache_license.txt. It is also available here:\r
- * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
- * \r
- * Any republication or derived work distributed in source code form\r
- * must include this copyright and license notice.\r
- */\r
-\r
-package compbio.engine;\r
-\r
-import static org.testng.Assert.assertEquals;\r
-import static org.testng.Assert.assertNotNull;\r
-import static org.testng.Assert.fail;\r
-\r
-import java.io.File;\r
-import java.io.IOException;\r
-import java.util.concurrent.TimeUnit;\r
-\r
-import org.testng.annotations.BeforeTest;\r
-import org.testng.annotations.Test;\r
-\r
-import compbio.engine.client.ConfiguredExecutable;\r
-import compbio.engine.client.Executable;\r
-import compbio.engine.local.AsyncLocalRunner;\r
-import compbio.metadata.AllTestSuit;\r
-import compbio.metadata.ChunkHolder;\r
-import compbio.metadata.JobSubmissionException;\r
-import compbio.metadata.ResultNotAvailableException;\r
-import compbio.runner.msa.ClustalW;\r
-import compbio.runner.msa.Muscle;\r
-\r
-public class FilePullerTester {\r
-\r
- public static String test_input = AllTestSuit.TEST_DATA_PATH_ABSOLUTE\r
- + "TO1381.fasta";\r
-\r
- String jobId;\r
- String jobId2;\r
- String jobId3;\r
-\r
- @BeforeTest(alwaysRun = true)\r
- public void init() {\r
- ClustalW clustal = new ClustalW();\r
- clustal.setInput(test_input);\r
- Muscle ms = new Muscle().setInput(test_input);\r
- Muscle ms2 = new Muscle().setInput(test_input);\r
-\r
- try {\r
- // For local execution use relavive\r
- ConfiguredExecutable<ClustalW> confClustal = Configurator\r
- .configureExecutable(clustal, Executable.ExecProvider.Local);\r
- ConfiguredExecutable<Muscle> confms = Configurator\r
- .configureExecutable(ms, Executable.ExecProvider.Local);\r
-\r
- ConfiguredExecutable<Muscle> confms2 = Configurator\r
- .configureExecutable(ms2, Executable.ExecProvider.Local);\r
-\r
- AsyncLocalRunner as = new AsyncLocalRunner();\r
- jobId = as.submitJob(confClustal);\r
- jobId2 = as.submitJob(confms);\r
- jobId3 = as.submitJob(confms2);\r
-\r
- ConfiguredExecutable<?> al = as.getResults(jobId);\r
- ConfiguredExecutable<?> al2 = as.getResults(jobId2);\r
- ConfiguredExecutable<?> al3 = as.getResults(jobId3);\r
- assertNotNull(al);\r
- assertNotNull(al2);\r
- assertNotNull(al3);\r
- } catch (JobSubmissionException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (ResultNotAvailableException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- }\r
- }\r
-\r
- @Test(groups = { AllTestSuit.test_group_engine })\r
- public void testPull() {\r
- assertNotNull(jobId, "init() method failed!");\r
- String workDir = Configurator.getWorkDirectory(jobId);\r
- String statFile = workDir + File.separator + ClustalW.getStatFile();\r
-\r
- ChunkHolder ch = ProgressGetter.pull(statFile, 0);\r
- while (ch == null) {\r
- ch = ProgressGetter.pull(statFile, 0);\r
- }\r
- String chunk = "";\r
- long pos = 0;\r
- do {\r
- chunk = ch.getChunk();\r
- assertNotNull(chunk);\r
- pos = ch.getNextPosition();\r
- ch = ProgressGetter.pull(statFile, pos);\r
- } while (chunk.length() > 0);\r
-\r
- // All consequent pulls just return empty chunk and same position =\r
- // file.length\r
- ch = ProgressGetter.pull(statFile, pos);\r
- assertNotNull(ch);\r
- assertEquals(ch.getChunk().length(), 0);\r
- // Output file size depends on the operation system fs!\r
- // assertEquals(ch.getNextPosition(), 668);\r
-\r
- ch = ProgressGetter.pull(statFile, pos);\r
- assertNotNull(ch);\r
- assertEquals(ch.getChunk().length(), 0);\r
- // Output file size depends on the operation system and fs!\r
- // assertEquals(ch.getNextPosition(), 668);\r
-\r
- }\r
-\r
- @Test(groups = { AllTestSuit.test_group_engine })\r
- public void testGetDelay() {\r
- FilePuller fp = FilePuller.newFilePuller(Configurator\r
- .getWorkDirectory(jobId)\r
- + File.separator + "stat.log", 256);\r
- // default delay is 5 minutes\r
- assertEquals(fp.getDelayValue(TimeUnit.SECONDS), 5 * 60);\r
- long d = 1000 * 1000 * 1000L * 60; // 1m in nanoseconds\r
- fp.setDelay(d, TimeUnit.NANOSECONDS);\r
- assertEquals(fp.getDelayValue(TimeUnit.NANOSECONDS), d);\r
- assertEquals(fp.getDelayValue(TimeUnit.SECONDS), 60);\r
- assertEquals(fp.getDelayValue(TimeUnit.MINUTES), 1);\r
- }\r
-\r
- @Test(groups = { AllTestSuit.test_group_engine }, dependsOnMethods = { "testPull" })\r
- public void testCache() {\r
- assertNotNull(jobId, "init() method failed!");\r
- assertNotNull(jobId2, "init() method failed!");\r
- assertEquals(PulledFileCache.getSize(), 1); // One is from previous test\r
-\r
- String statFile = Configurator.getWorkDirectory(jobId) + File.separator\r
- + ClustalW.getStatFile();\r
- String statFile2 = Configurator.getWorkDirectory(jobId2)\r
- + File.separator + Muscle.getStatFile();\r
- String statFile3 = Configurator.getWorkDirectory(jobId3)\r
- + File.separator + Muscle.getStatFile();\r
-\r
- ChunkHolder ch = ProgressGetter.pull(statFile, 0);\r
- assertEquals(PulledFileCache.getSize(), 1); // Still one as job has been\r
- // retrieved from cache\r
- ChunkHolder ch2 = ProgressGetter\r
- .pull(statFile2, 0, 5, TimeUnit.SECONDS); // 5\r
- // second delay\r
- assertEquals(PulledFileCache.getSize(), 2); // One is from previous test\r
-\r
- // Pull the first job completely\r
- while (ch == null) {\r
- ch = ProgressGetter.pull(statFile, 0);\r
- }\r
- String chunk = "";\r
- long pos = 0;\r
- do {\r
- chunk = ch.getChunk();\r
- assertNotNull(chunk);\r
- pos = ch.getNextPosition();\r
- ch = ProgressGetter.pull(statFile, pos);\r
- } while (chunk.length() > 0);\r
-\r
- try {\r
- Thread.sleep(1000 * 6);\r
- } catch (InterruptedException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- }\r
- // Elements are removed on put operation only\r
- assertEquals(PulledFileCache.getSize(), 2); // One is from previous test\r
- ChunkHolder ch3 = ProgressGetter.pull(statFile3, 0);\r
- // Now old element was removed, but new added, thus size remains\r
- // constant\r
- assertEquals(PulledFileCache.getSize(), 2); // One is from previous test\r
-\r
- }\r
-\r
- @Test\r
- public void testGet() {\r
-\r
- FilePuller pp = FilePuller\r
- .newProgressPuller(AllTestSuit.TEST_DATA_PATH_ABSOLUTE\r
- + "percentProgress.txt");\r
- try {\r
- assertEquals(pp.getProgress(), 12);\r
- pp.disconnect();\r
- } catch (NumberFormatException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- } catch (IOException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- }\r
- }\r
-}\r
+++ /dev/null
-package compbio.engine;\r
-\r
-import static org.testng.Assert.assertEquals;\r
-import static org.testng.Assert.assertNotNull;\r
-import static org.testng.Assert.assertTrue;\r
-import static org.testng.Assert.fail;\r
-\r
-import java.io.FileInputStream;\r
-import java.io.IOException;\r
-import java.util.List;\r
-\r
-import org.testng.annotations.Test;\r
-\r
-import compbio.data.sequence.FastaSequence;\r
-import compbio.data.sequence.SequenceUtil;\r
-import compbio.engine.client.ConfiguredExecutable;\r
-import compbio.engine.client.Executable.ExecProvider;\r
-import compbio.metadata.AllTestSuit;\r
-import compbio.metadata.JobSubmissionException;\r
-import compbio.metadata.Limit;\r
-import compbio.metadata.PresetManager;\r
-import compbio.runner.msa.ClustalW;\r
-\r
-public class LoadBalancerTester {\r
-\r
- @Test\r
- public void testLoadBalance() {\r
- /**\r
- * This is 5 sequence x per 20000 length\r
- */\r
- String test_input = AllTestSuit.TEST_DATA_PATH_ABSOLUTE\r
- + "testlimit.fasta";\r
- try {\r
- FileInputStream fio = new FileInputStream(test_input);\r
- List<FastaSequence> data = SequenceUtil.readFasta(fio);\r
- fio.close();\r
- assertNotNull(data);\r
- assertTrue(data.size() > 0);\r
-\r
- ClustalW clustal = new ClustalW();\r
- /**\r
- * ClustalW local limit is 2 sequences per 500 letters\r
- */\r
- ConfiguredExecutable<ClustalW> confClust = Configurator\r
- .configureExecutable(clustal);\r
- ExecProvider aEngine = LoadBalancer.getEngine(confClust, data);\r
- Limit<ClustalW> locExec = new Limit<ClustalW>(2, 500, PresetManager.LOCAL_ENGINE_LIMIT_PRESET); \r
- // For testing of production configuration uncomment\r
- //Limit locExec = confClust\r
- // .getLimit(PresetManager.LOCAL_ENGINE_LIMIT_PRESET);\r
- assertTrue(locExec.getSeqNumber() <= data.size()\r
- || locExec.getAvgSeqLength() * locExec.getSeqNumber() <= Limit\r
- .getAvgSequenceLength(data));\r
- // Engine will be local because LoadBalancer accessed the presets & limits \r
- // directly\r
- // For testing of production configuration uncomment\r
- // assertEquals(aEngine, ExecProvider.Cluster);\r
-\r
- } catch (JobSubmissionException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- } catch (IOException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- }\r
-\r
- }\r
-}\r
+++ /dev/null
-/* Copyright (c) 2009 Peter Troshin\r
- * \r
- * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0 \r
- * \r
- * This library is free software; you can redistribute it and/or modify it under the terms of the\r
- * Apache License version 2 as published by the Apache Software Foundation\r
- * \r
- * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
- * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
- * License for more details.\r
- * \r
- * A copy of the license is in apache_license.txt. It is also available here:\r
- * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
- * \r
- * Any republication or derived work distributed in source code form\r
- * must include this copyright and license notice.\r
- */\r
-\r
-package compbio.engine;\r
-\r
-import static org.testng.Assert.assertEquals;\r
-import static org.testng.Assert.assertNotNull;\r
-import static org.testng.Assert.fail;\r
-\r
-import java.util.concurrent.TimeUnit;\r
-\r
-import org.testng.annotations.Test;\r
-\r
-import compbio.metadata.AllTestSuit;\r
-\r
-public class PulledFileCacheTester {\r
-\r
- @Test\r
- public void test() {\r
- try {\r
- FilePuller fp1 = FilePuller.newFilePuller(\r
- AllTestSuit.TEST_DATA_PATH_ABSOLUTE + "1", 256);\r
- fp1.setDelay(2, TimeUnit.SECONDS);\r
-\r
- FilePuller fp2 = FilePuller.newFilePuller(\r
- AllTestSuit.TEST_DATA_PATH_ABSOLUTE + "2", 256);\r
- fp2.setDelay(1, TimeUnit.SECONDS);\r
-\r
- FilePuller fp3 = FilePuller.newFilePuller(\r
- AllTestSuit.TEST_DATA_PATH_ABSOLUTE + "3", 256);\r
- fp3.setDelay(1, TimeUnit.SECONDS);\r
-\r
- FilePuller fp4 = FilePuller.newFilePuller(\r
- AllTestSuit.TEST_DATA_PATH_ABSOLUTE + "4", 256);\r
- fp4.setDelay(5, TimeUnit.SECONDS);\r
-\r
- // This only hold if tested in isolation thus clear is essential\r
- PulledFileCache.clear();\r
- assertEquals(PulledFileCache.getSize(), 0);\r
- PulledFileCache.put(fp1);\r
- PulledFileCache.put(fp2);\r
- PulledFileCache.put(fp3);\r
- PulledFileCache.put(fp4);\r
- assertEquals(PulledFileCache.getSize(), 4);\r
- Thread.sleep(1000);\r
- // sweep was not called yet\r
- assertEquals(PulledFileCache.getSize(), 4);\r
- // now sweep is called\r
- PulledFileCache.put(fp1);\r
- // fp1 and fp1 and fp4 only remains - copies are allowed this is\r
- // responsibility of the caller to ensure they are not there\r
- assertEquals(PulledFileCache.getSize(), 3);\r
- assertNotNull(PulledFileCache\r
- .get(AllTestSuit.TEST_DATA_PATH_ABSOLUTE + "1"));\r
- assertNotNull(PulledFileCache\r
- .get(AllTestSuit.TEST_DATA_PATH_ABSOLUTE + "4"));\r
-\r
- for (int i = 0; i < 4; i++) {\r
- Thread.sleep(1000);\r
- FilePuller fp = PulledFileCache\r
- .get(AllTestSuit.TEST_DATA_PATH_ABSOLUTE + "4");\r
- // This will update access time\r
- fp.isFileCreated();\r
- }\r
- // still fp1 and fp4 only remains\r
-\r
- assertEquals(PulledFileCache.getSize(), 3);\r
- PulledFileCache.put(FilePuller.newFilePuller(\r
- AllTestSuit.TEST_DATA_PATH_ABSOLUTE + "5", 256));\r
- // at this point only fp4 and 5 will remain\r
- assertEquals(PulledFileCache.getSize(), 2);\r
- assertNotNull(PulledFileCache\r
- .get(AllTestSuit.TEST_DATA_PATH_ABSOLUTE + "4"));\r
- assertNotNull(PulledFileCache\r
- .get(AllTestSuit.TEST_DATA_PATH_ABSOLUTE + "5"));\r
-\r
- } catch (InterruptedException e) {\r
- fail(e.getMessage());\r
- }\r
- }\r
-\r
-}\r
+++ /dev/null
-/* Copyright (c) 2009 Peter Troshin\r
- * \r
- * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0 \r
- * \r
- * This library is free software; you can redistribute it and/or modify it under the terms of the\r
- * Apache License version 2 as published by the Apache Software Foundation\r
- * \r
- * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
- * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
- * License for more details.\r
- * \r
- * A copy of the license is in apache_license.txt. It is also available here:\r
- * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
- * \r
- * Any republication or derived work distributed in source code form\r
- * must include this copyright and license notice.\r
- */\r
-\r
-package compbio.engine.client;\r
-\r
-import static org.testng.Assert.assertEquals;\r
-import static org.testng.Assert.assertFalse;\r
-import static org.testng.Assert.assertNotSame;\r
-import static org.testng.Assert.assertTrue;\r
-import static org.testng.Assert.fail;\r
-\r
-import java.io.FileNotFoundException;\r
-import java.io.IOException;\r
-import java.util.Arrays;\r
-import java.util.List;\r
-\r
-import org.testng.annotations.Test;\r
-\r
-import compbio.metadata.RunnerConfig;\r
-import compbio.runner.msa.ClustalW;\r
-import compbio.runner.msa.Mafft;\r
-import compbio.runner.msa.Muscle;\r
-\r
-public class CommandBuilderTester {\r
-\r
- @Test()\r
- public void testCommandBuilding() {\r
- CommandBuilder<ClustalW> builder = new CommandBuilder<ClustalW>("=");\r
- builder.setParam("-MATRIX", "blosum65");\r
- assertTrue(builder.getCommands().size() == 1);\r
- String p = builder.getParamValue("-MATRIX");\r
- builder.setParam("-clustalw");\r
- builder.setParam("-in", "\\gile\\path\\abs.txt");\r
- System.out.println(builder.getCommands());\r
- assertTrue(builder.getCommands().size() == 3);\r
- builder.setParam("-stat=/test.log");\r
- assertTrue(builder.getCommands().size() == 4);\r
- System.out.println("CP:" + builder.getCommands());\r
- assertTrue(builder.setParam("-stat=/newtest.log"));\r
-\r
- List<String> clist = Arrays.asList("-prop", "-tree=treefile.txt",\r
- "-clustalw");\r
- builder.addParams(clist);\r
- assertTrue(builder.size() == 6);\r
- builder.setParams(clist);\r
- assertTrue(builder.size() == 3);\r
- System.out.println("CP:" + builder.getCommands());\r
- String option = "-log=error.txt";\r
- builder.setFirst(option);\r
- assertEquals(builder.getCommands().get(0), option);\r
- builder.setParam("-newParam2");\r
- assertEquals(builder.getCommands().get(0), option);\r
- builder.setLast(option);\r
- assertNotSame(builder.getCommands().get(0), option);\r
- assertEquals(builder.getCommands().get(builder.size() - 1), option);\r
- builder.setParam("-newParam3");\r
- assertEquals(builder.getCommands().get(builder.size() - 1), option);\r
- builder.setParam("-prm5", "prm5Value");\r
- assertTrue(builder.hasParam("-prm5"));\r
- }\r
-\r
- @Test\r
- public void testSpaceDelimiterExecutable() {\r
- CommandBuilder<Muscle> cbuilder = new CommandBuilder<Muscle>(" ");\r
- cbuilder.addParams(Arrays.asList("-clwstrict", "-quiet", "-verbose",\r
- "-log", "EXEC_STAT_FILE"));\r
- }\r
-\r
- @Test\r
- public void testOptionsToCommand() {\r
- try {\r
- RunnerConfig<Mafft> rconf = ConfExecutable\r
- .getRunnerOptions(Mafft.class);\r
- CommandBuilder<Mafft> cbuilder = CommandBuilder.newCommandBuilder(\r
- rconf.getArguments(), Mafft.KEY_VALUE_SEPARATOR);\r
- String comm = "";\r
- for (String val : cbuilder.getCommands()) {\r
- assertFalse(val.contains(cbuilder.nameValueSeparator));\r
- comm += val + cbuilder.nameValueSeparator;\r
- }\r
- assertEquals(cbuilder.getCommandString(), comm);\r
- } catch (FileNotFoundException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (IOException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- }\r
-\r
- }\r
-}\r
+++ /dev/null
-/* Copyright (c) 2009 Peter Troshin\r
- * \r
- * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0 \r
- * \r
- * This library is free software; you can redistribute it and/or modify it under the terms of the\r
- * Apache License version 2 as published by the Apache Software Foundation\r
- * \r
- * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
- * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
- * License for more details.\r
- * \r
- * A copy of the license is in apache_license.txt. It is also available here:\r
- * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
- * \r
- * Any republication or derived work distributed in source code form\r
- * must include this copyright and license notice.\r
- */\r
-\r
-package compbio.engine.client;\r
-\r
-import static org.testng.Assert.assertFalse;\r
-import static org.testng.Assert.assertTrue;\r
-import static org.testng.Assert.fail;\r
-\r
-import java.io.File;\r
-import java.io.IOException;\r
-import java.net.URISyntaxException;\r
-import java.net.URL;\r
-\r
-import org.testng.annotations.Test;\r
-\r
-import compbio.engine.client.PathValidator;\r
-import compbio.runner.msa.ClustalW;\r
-import compbio.util.SysPrefs;\r
-\r
-public class PathValidatorTester {\r
-\r
- @Test\r
- public void testIsAbsolutePath() {\r
-\r
- if (SysPrefs.isWindows) {\r
- /*\r
- * slash(\) has to be prefixed with another slash to produce a\r
- * single slash\r
- */\r
- assertTrue(PathValidator.isAbsolutePath("d:\\temp"));\r
- assertFalse(PathValidator.isAbsolutePath("/home"));\r
- } else {\r
- assertFalse(PathValidator.isAbsolutePath("d:\\temp"));\r
- assertTrue(PathValidator.isAbsolutePath("/home"));\r
- }\r
- assertFalse(PathValidator.isAbsolutePath("home"));\r
- }\r
-\r
- @Test\r
- public void testGetClassPath() {\r
- String clname = ClustalW.class.getSimpleName();\r
- System.out.println("%" + clname);\r
- URL url = ClustalW.class.getResource(clname + ".class");\r
- URL url2 = ClassLoader.getSystemResource("Engine.local.properties");\r
-\r
- try {\r
- File f = new File(url.toURI());\r
- System.out.println("&" + f.getAbsolutePath());\r
- System.out.println("&" + f.getCanonicalPath());\r
- System.out.println("&" + f.getParent());\r
- } catch (URISyntaxException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (IOException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- }\r
- System.out.println("!!" + url2);\r
- System.out.println("!" + url.getFile());\r
- System.out.println("!" + System.getProperty("java.class.path", null));\r
-\r
- }\r
-}\r
+++ /dev/null
-/* Copyright (c) 2009 Peter Troshin\r
- * \r
- * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0 \r
- * \r
- * This library is free software; you can redistribute it and/or modify it under the terms of the\r
- * Apache License version 2 as published by the Apache Software Foundation\r
- * \r
- * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
- * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
- * License for more details.\r
- * \r
- * A copy of the license is in apache_license.txt. It is also available here:\r
- * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
- * \r
- * Any republication or derived work distributed in source code form\r
- * must include this copyright and license notice.\r
- */\r
-\r
-package compbio.engine.cluster.drmaa;\r
-\r
-import static org.testng.Assert.assertEquals;\r
-import static org.testng.Assert.assertFalse;\r
-import static org.testng.Assert.assertTrue;\r
-import static org.testng.Assert.fail;\r
-\r
-import org.testng.annotations.Test;\r
-\r
-import compbio.engine.AsyncExecutor;\r
-import compbio.engine.Configurator;\r
-import compbio.engine.Job;\r
-import compbio.engine.client.ConfiguredExecutable;\r
-import compbio.engine.client.Executable;\r
-import compbio.metadata.AllTestSuit;\r
-import compbio.metadata.JobSubmissionException;\r
-import compbio.metadata.ResultNotAvailableException;\r
-import compbio.runner.msa.ClustalW;\r
-import compbio.util.Util;\r
-\r
-public class ClusterSessionTester {\r
-\r
- @Test(sequential = true, groups = { AllTestSuit.test_group_cluster,\r
- AllTestSuit.test_group_engine })\r
- public void testTaskList() {\r
- ClustalW cl = new ClustalW();\r
-\r
- try {\r
- ConfiguredExecutable<ClustalW> clw = Configurator\r
- .configureExecutable(cl, Executable.ExecProvider.Cluster);\r
- ClusterRunner jr = ClusterRunner.getInstance(clw);\r
- String jobId = jr.submitJob();\r
- ClusterSession cs = ClusterSession.getInstance();\r
- // this only holds for sequential execution\r
- //assertEquals(cs.jobs.size(), 1);\r
- assertTrue(Job.getByTaskId(jobId, cs.jobs) != null);\r
- assertEquals(Job.getByTaskId(jobId, cs.jobs).getConfExecutable(),\r
- clw);\r
- jr.cancelJob(jobId);\r
- // this only holds for sequential execution\r
- assertEquals(cs.jobs.size(), 0);\r
-\r
- clw = Configurator.configureExecutable(cl,\r
- Executable.ExecProvider.Cluster);\r
- assertFalse(Util.isEmpty(clw.getWorkDirectory()));\r
- AsyncExecutor aengine = Configurator.getAsyncEngine(clw);\r
- jobId = aengine.submitJob(clw);\r
- assertEquals(cs.jobs.size(), 1);\r
- assertTrue(Job.getByTaskId(jobId, cs.jobs) != null);\r
- assertEquals(Job.getByTaskId(jobId, cs.jobs).getConfExecutable(),\r
- clw);\r
- assertFalse(Util.isEmpty(compbio.engine.Configurator\r
- .getWorkDirectory(jobId)));\r
- String workDir = clw.getWorkDirectory();\r
- assertEquals(workDir, compbio.engine.Configurator\r
- .getWorkDirectory(jobId));\r
-\r
- aengine.getResults(jobId);\r
- assertEquals(cs.jobs.size(), 0);\r
- assertFalse(Util.isEmpty(clw.getWorkDirectory()));\r
- // after job has been removed from the list (e.g when completed)\r
- // reference to a work directory can still be obtained by other\r
- // means\r
- assertFalse(Util.isEmpty(compbio.engine.Configurator\r
- .getWorkDirectory(jobId)));\r
- assertEquals(compbio.engine.Configurator.getWorkDirectory(jobId),\r
- workDir);\r
-\r
- } catch (JobSubmissionException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- } catch (ResultNotAvailableException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- }\r
- }\r
-\r
-}\r
+++ /dev/null
-/* Copyright (c) 2009 Peter Troshin\r
- * \r
- * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0 \r
- * \r
- * This library is free software; you can redistribute it and/or modify it under the terms of the\r
- * Apache License version 2 as published by the Apache Software Foundation\r
- * \r
- * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
- * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
- * License for more details.\r
- * \r
- * A copy of the license is in apache_license.txt. It is also available here:\r
- * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
- * \r
- * Any republication or derived work distributed in source code form\r
- * must include this copyright and license notice.\r
- */\r
-\r
-package compbio.engine.cluster.drmaa;\r
-\r
-import static org.testng.AssertJUnit.assertEquals;\r
-import static org.testng.AssertJUnit.assertFalse;\r
-import static org.testng.AssertJUnit.assertNotNull;\r
-import static org.testng.AssertJUnit.assertNull;\r
-import static org.testng.AssertJUnit.assertTrue;\r
-import static org.testng.AssertJUnit.fail;\r
-\r
-import org.testng.annotations.Test;\r
-\r
-import compbio.engine.AsyncExecutor;\r
-import compbio.engine.Configurator;\r
-import compbio.engine.client.ConfiguredExecutable;\r
-import compbio.engine.client.Executable;\r
-import compbio.metadata.AllTestSuit;\r
-import compbio.metadata.JobStatus;\r
-import compbio.metadata.JobSubmissionException;\r
-import compbio.metadata.ResultNotAvailableException;\r
-import compbio.runner.msa.ClustalW;\r
-import compbio.util.SysPrefs;\r
-\r
-public class DrmaaAsyncClusterEngineTester {\r
-\r
- public static String test_input = AllTestSuit.TEST_DATA_PATH_ABSOLUTE\r
- + "TO1381.fasta";\r
- public static String large_test_input = AllTestSuit.TEST_DATA_PATH_ABSOLUTE\r
- + "1000x3000Dna.fasta";\r
- public static String cluster_test_outfile = "TO1381.clustal.cluster.out";\r
-\r
- /**\r
- * This test uses ClustalW executable as runnable to testing, thus depends\r
- * on its correct functioning\r
- */\r
- @Test(groups = { AllTestSuit.test_group_cluster,\r
- AllTestSuit.test_group_engine })\r
- public void testSubmit() {\r
- ClustalW clustal = new ClustalW();\r
- assertFalse("Cluster execution can only be in unix environment",\r
- SysPrefs.isWindows);\r
- clustal.setInput(test_input).setOutput(cluster_test_outfile);\r
- try {\r
- ConfiguredExecutable<ClustalW> confClustal = Configurator\r
- .configureExecutable(clustal);\r
- AsyncExecutor runner = new AsyncClusterRunner();\r
- assertNotNull("Runner is NULL", runner);\r
- String jobId = runner.submitJob(confClustal);\r
- assertEquals("Input was not set!", test_input, clustal.getInput());\r
- assertNotNull("JobId is null", jobId);\r
- JobStatus status = runner.getJobStatus(jobId);\r
- assertTrue("Status of the process is wrong!",\r
- status == JobStatus.PENDING || status == JobStatus.RUNNING);\r
- JobStatus info = runner.getJobStatus(jobId);\r
- assertNotNull("JobInfo is null", info);\r
- Executable<?> result = runner.getResults(jobId);\r
-\r
- } catch (JobSubmissionException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- } catch (ResultNotAvailableException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- }\r
- }\r
-\r
- @Test(expectedExceptions = ResultNotAvailableException.class, groups = {\r
- AllTestSuit.test_group_cluster, AllTestSuit.test_group_engine })\r
- // expectedExceptions = ResultNotAvailableException.class,\r
- public void testCancel() throws ResultNotAvailableException {\r
- ClustalW clustal = new ClustalW();\r
- assertFalse("Cluster execution can only be in unix environment",\r
- SysPrefs.isWindows);\r
- clustal.setInput(large_test_input).setOutput(cluster_test_outfile);\r
-\r
- try {\r
- ConfiguredExecutable<ClustalW> confClustal = Configurator\r
- .configureExecutable(clustal);\r
- AsyncClusterRunner runner = new AsyncClusterRunner();\r
- String jobId = runner.submitJob(confClustal);\r
- assertNotNull("Runner is NULL", runner);\r
- // assertNotNull("JobId is null", jobId1);\r
- Thread.sleep(200);\r
- JobStatus status = runner.getJobStatus(jobId);\r
- assertTrue("Status of the process is wrong!",\r
- status == JobStatus.PENDING || status == JobStatus.RUNNING);\r
- assertFalse("Status of the process is wrong!",\r
- status == JobStatus.FINISHED);\r
- runner.cancelJob(jobId);\r
- // This is never NULL as long as the job has started!\r
- ConfiguredExecutable<?> exec = runner.getResults(jobId);\r
- assertNull(exec.getResults());\r
- } catch (JobSubmissionException e) {\r
- e.printStackTrace();\r
- fail("DrmaaException caught:" + e.getMessage());\r
- } catch (InterruptedException e) {\r
- e.printStackTrace();\r
- fail("Interupted exception caught:" + e.getMessage());\r
- }\r
- }\r
-\r
- @Test(groups = { AllTestSuit.test_group_cluster,\r
- AllTestSuit.test_group_engine })\r
- public void testGetJobStatus() {\r
- ClustalW clustal = new ClustalW();\r
- assertFalse("Cluster execution can only be in unix environment",\r
- SysPrefs.isWindows);\r
- clustal.setInput(test_input).setOutput(cluster_test_outfile);\r
-\r
- try {\r
- AsyncClusterRunner runner = new AsyncClusterRunner();\r
- ConfiguredExecutable<ClustalW> confClustal = Configurator\r
- .configureExecutable(clustal);\r
- String jobId = runner.submitJob(confClustal);\r
- assertNotNull("Runner is NULL", runner);\r
- AsyncClusterRunner runner2 = new AsyncClusterRunner();\r
-\r
- boolean hasRun = false;\r
- boolean hasPended = false;\r
- Thread.sleep(500); \r
- JobStatus status = runner2.getJobStatus(jobId);\r
- while (status != JobStatus.FINISHED) {\r
- if (status == JobStatus.CANCELLED) {\r
- fail("Job is not cancelled!");\r
- }\r
- if (status == JobStatus.FAILED) {\r
- fail("Job should not fail!");\r
- }\r
- if (status == JobStatus.RUNNING) {\r
- hasRun = true;\r
- }\r
- if (status == JobStatus.PENDING) {\r
- hasPended = true;\r
- }\r
- if (status == JobStatus.UNDEFINED) {\r
- System.out.println("Wrong status (UNDEFINED) reported by cluster engine!");\r
- break;\r
- }\r
- status = runner2.getJobStatus(jobId);\r
- }\r
- assertTrue(hasRun);\r
- assertTrue(hasPended);\r
- assertTrue(hasRun);\r
- // Bear in mind that if the task were not put in the queue\r
- // immediately\r
- // the status could be UNDEFINED!\r
- // assertFalse(hasUndefined);\r
- AsyncClusterRunner runner3 = new AsyncClusterRunner();\r
- Executable<?> exec = runner3.getResults(jobId);\r
- assertNotNull(exec);\r
- // Now try collecting result for the second time\r
- exec=null;\r
- Thread.sleep(1000);\r
- exec = runner3.getResults(jobId);\r
- assertNotNull(exec);\r
- } catch (JobSubmissionException e) {\r
- e.printStackTrace();\r
- fail("DrmaaException caught:" + e.getMessage());\r
- } catch (ResultNotAvailableException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- } catch (InterruptedException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- }\r
- }\r
-}\r
+++ /dev/null
-/* Copyright (c) 2009 Peter Troshin\r
- * \r
- * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0 \r
- * \r
- * This library is free software; you can redistribute it and/or modify it under the terms of the\r
- * Apache License version 2 as published by the Apache Software Foundation\r
- * \r
- * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
- * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
- * License for more details.\r
- * \r
- * A copy of the license is in apache_license.txt. It is also available here:\r
- * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
- * \r
- * Any republication or derived work distributed in source code form\r
- * must include this copyright and license notice.\r
- */\r
-\r
-package compbio.engine.cluster.drmaa;\r
-\r
-import static org.testng.AssertJUnit.assertEquals;\r
-import static org.testng.AssertJUnit.assertFalse;\r
-import static org.testng.AssertJUnit.assertNotNull;\r
-import static org.testng.AssertJUnit.assertTrue;\r
-import static org.testng.AssertJUnit.fail;\r
-\r
-import java.text.ParseException;\r
-\r
-import org.ggf.drmaa.DrmaaException;\r
-import org.ggf.drmaa.JobInfo;\r
-import org.testng.annotations.Test;\r
-\r
-import compbio.data.sequence.Alignment;\r
-import compbio.engine.Configurator;\r
-import compbio.engine.client.ConfiguredExecutable;\r
-import compbio.engine.client.Executable;\r
-import compbio.engine.client.EngineUtil;\r
-import compbio.metadata.AllTestSuit;\r
-import compbio.metadata.JobExecutionException;\r
-import compbio.metadata.JobStatus;\r
-import compbio.metadata.JobSubmissionException;\r
-import compbio.metadata.ResultNotAvailableException;\r
-import compbio.runner.msa.ClustalW;\r
-import compbio.util.SysPrefs;\r
-\r
-public class DrmaaClusterEngineTester {\r
-\r
- public static String test_input = AllTestSuit.TEST_DATA_PATH_ABSOLUTE\r
- + "TO1381.fasta";\r
- public static String cluster_test_outfile = "TO1381.clustal.cluster.out";\r
-\r
- /**\r
- * This test uses ClustalW executable as runnable to testing, thus depends\r
- * on its correct functioning\r
- */\r
- @Test(groups = { AllTestSuit.test_group_cluster,\r
- AllTestSuit.test_group_engine })\r
- public void testSubmit() {\r
- ClustalW clustal = new ClustalW();\r
- assertFalse("Cluster execution can only be in unix environment",\r
- SysPrefs.isWindows);\r
- clustal.setInput(test_input).setOutput(cluster_test_outfile);\r
-\r
- try {\r
- ConfiguredExecutable<ClustalW> confClust = Configurator\r
- .configureExecutable(clustal,\r
- Executable.ExecProvider.Cluster);\r
- assertNotNull(confClust.getWorkDirectory());\r
-\r
- ClusterRunner runner = ClusterRunner.getInstance(confClust);\r
- assertEquals("Input was not set!", test_input, clustal.getInput());\r
- assertNotNull("Runner is NULL", runner);\r
- runner.executeJob();\r
- // assertNotNull("JobId is null", jobId1);\r
- JobStatus status = runner.getJobStatus();\r
- assertTrue("Status of the process is wrong!",\r
- status == JobStatus.PENDING || status == JobStatus.RUNNING);\r
- JobInfo info = runner.getJobInfo();\r
-\r
- assertFalse(EngineUtil.isMarked(confClust.getWorkDirectory(),\r
- JobStatus.CANCELLED));\r
- assertFalse(EngineUtil.isMarked(confClust.getWorkDirectory(),\r
- JobStatus.STARTED));\r
- assertFalse(EngineUtil.isMarked(confClust.getWorkDirectory(),\r
- JobStatus.COLLECTED));\r
- assertTrue(EngineUtil.isMarked(confClust.getWorkDirectory(),\r
- JobStatus.FINISHED));\r
- assertTrue(EngineUtil.isMarked(confClust.getWorkDirectory(),\r
- JobStatus.SUBMITTED));\r
-\r
- ConfiguredExecutable<?> confExec = runner.waitForResult();\r
- // At this point results are marked as collected\r
- assertTrue(EngineUtil.isMarked(confClust.getWorkDirectory(),\r
- JobStatus.COLLECTED));\r
-\r
- assertNotNull("JobInfo is null", info);\r
- StatisticManager sm = new StatisticManager(info);\r
- assertNotNull("Statistics manager is null", sm);\r
-\r
- try {\r
-\r
- String exits = sm.getExitStatus();\r
- assertNotNull("Exit status is null", exits);\r
- // cut 4 trailing zeros from the number\r
- int exitsInt = ClusterEngineUtil.CLUSTER_STAT_IN_SEC.parse(exits)\r
- .intValue();\r
- assertEquals("Exit status is not 0", 0, exitsInt);\r
- System.out.println(sm.getAllStats());\r
-\r
- } catch (ParseException e) {\r
- e.printStackTrace();\r
- fail("Parse Exception: " + e.getMessage());\r
- }\r
- assertTrue("Process exited:", sm.hasExited());\r
- assertFalse("Process aborted:", sm.wasAborted());\r
- assertFalse("Process hasdump:", sm.hasDump());\r
- assertFalse("Process signaled:", sm.hasSignaled());\r
-\r
- Alignment al = confExec.getResults();\r
- assertNotNull(al);\r
- assertFalse("Could not remove some files whilst cleaning up ",\r
- runner.cleanup());\r
-\r
- } catch (JobSubmissionException e) {\r
- e.printStackTrace();\r
- fail("DrmaaException caught:" + e.getMessage());\r
- } catch (JobExecutionException e) {\r
- e.printStackTrace();\r
- fail("DrmaaException caught:" + e.getMessage());\r
- } catch (DrmaaException e) {\r
- e.printStackTrace();\r
- fail("DrmaaException caught:" + e.getMessage());\r
- } catch (ResultNotAvailableException e) {\r
- fail("DrmaaException caught:" + e.getMessage());\r
- }\r
- }\r
-\r
- @Test(groups = { AllTestSuit.test_group_cluster,\r
- AllTestSuit.test_group_engine })\r
- public void testCancel() {\r
- ClustalW clustal = new ClustalW();\r
- assertFalse("Cluster execution can only be in unix environment",\r
- SysPrefs.isWindows);\r
- clustal.setInput(test_input).setOutput(cluster_test_outfile);\r
-\r
- try {\r
-\r
- ConfiguredExecutable<ClustalW> confClust = Configurator\r
- .configureExecutable(clustal,\r
- Executable.ExecProvider.Cluster);\r
- assertNotNull(confClust.getWorkDirectory());\r
-\r
- ClusterRunner runner = ClusterRunner.getInstance(confClust);\r
- assertNotNull("Runner is NULL", runner);\r
-\r
- runner.executeJob();\r
- // assertNotNull("JobId is null", jobId1);\r
- Thread.sleep(500);\r
- JobStatus status = runner.getJobStatus();\r
- assertTrue("Status of the process is wrong!",\r
- status == JobStatus.PENDING || status == JobStatus.RUNNING);\r
- runner.cancelJob();\r
- Thread.sleep(200); // give fs time to write a file\r
- JobInfo info = runner.getJobInfo();\r
- assertTrue(EngineUtil.isMarked(confClust.getWorkDirectory(),\r
- JobStatus.CANCELLED));\r
- assertFalse(EngineUtil.isMarked(confClust.getWorkDirectory(),\r
- JobStatus.STARTED));\r
- assertFalse(EngineUtil.isMarked(confClust.getWorkDirectory(),\r
- JobStatus.COLLECTED));\r
- assertTrue(EngineUtil.isMarked(confClust.getWorkDirectory(),\r
- JobStatus.FINISHED));\r
- assertTrue(EngineUtil.isMarked(confClust.getWorkDirectory(),\r
- JobStatus.SUBMITTED));\r
-\r
- } catch (JobSubmissionException e) {\r
- e.printStackTrace();\r
- fail("DrmaaException caught:" + e.getMessage());\r
- } catch (JobExecutionException e) {\r
- e.printStackTrace();\r
- fail("DrmaaException caught:" + e.getMessage());\r
- } catch (InterruptedException e) {\r
- e.printStackTrace();\r
- fail("Interupted exception caught:" + e.getMessage());\r
- }\r
- }\r
-\r
-}\r
+++ /dev/null
-/* Copyright (c) 2009 Peter Troshin\r
- * \r
- * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0 \r
- * \r
- * This library is free software; you can redistribute it and/or modify it under the terms of the\r
- * Apache License version 2 as published by the Apache Software Foundation\r
- * \r
- * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
- * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
- * License for more details.\r
- * \r
- * A copy of the license is in apache_license.txt. It is also available here:\r
- * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
- * \r
- * Any republication or derived work distributed in source code form\r
- * must include this copyright and license notice.\r
- */\r
-\r
-package compbio.engine.cluster.drmaa;\r
-\r
-import static org.testng.AssertJUnit.assertEquals;\r
-import static org.testng.AssertJUnit.assertNotNull;\r
-import static org.testng.AssertJUnit.fail;\r
-\r
-import java.text.ParseException;\r
-\r
-import org.testng.annotations.Test;\r
-\r
-import compbio.engine.cluster.drmaa.ClusterEngineUtil;\r
-\r
-public class UtilTester {\r
-\r
- @Test\r
- public void testParser() {\r
- try {\r
- Number n = ClusterEngineUtil.CLUSTER_STAT_IN_SEC.parse("11.0000");\r
- assertNotNull(n);\r
- int t = n.intValue();\r
- assertEquals(11, t);\r
- n = ClusterEngineUtil.CLUSTER_STAT_IN_SEC.parse("11.2300");\r
- assertNotNull(n);\r
- t = n.intValue();\r
- assertEquals(11, t);\r
- float f = n.floatValue();\r
- assertEquals(11.23f, f);\r
- n = ClusterEngineUtil.CLUSTER_STAT_IN_SEC.parse("0.0310");\r
- assertNotNull(n);\r
- f = n.floatValue();\r
- assertEquals(0.031f, f);\r
- } catch (ParseException e) {\r
- e.printStackTrace();\r
- fail("Parsing failed: " + e.getMessage());\r
- }\r
-\r
- }\r
-}\r
+++ /dev/null
-/* Copyright (c) 2009 Peter Troshin\r
- * \r
- * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0 \r
- * \r
- * This library is free software; you can redistribute it and/or modify it under the terms of the\r
- * Apache License version 2 as published by the Apache Software Foundation\r
- * \r
- * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
- * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
- * License for more details.\r
- * \r
- * A copy of the license is in apache_license.txt. It is also available here:\r
- * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
- * \r
- * Any republication or derived work distributed in source code form\r
- * must include this copyright and license notice.\r
- */\r
-\r
-package compbio.engine.conf;\r
-\r
-import static org.testng.Assert.assertEquals;\r
-import static org.testng.Assert.assertTrue;\r
-\r
-import java.util.HashSet;\r
-import java.util.Set;\r
-\r
-import org.testng.annotations.Test;\r
-\r
-import compbio.runner.msa.ClustalW;\r
-import compbio.util.SysPrefs;\r
-\r
-public class DirectoryManagerTester {\r
-\r
- @Test(invocationCount = 4, threadPoolSize = 4, sequential = false)\r
- public void testGetDirectory() {\r
- Set<Long> set = new HashSet<Long>();\r
- for (int i = 0; i < 20000; i++) {\r
- long number = DirectoryManager.getNonRepeatableNumber();\r
- assertTrue(set.add(number));\r
- // Cannot rely on the length is the returned long, as precision is\r
- // implementation dependent\r
- // see testNanoTime method below\r
- // assertEquals(Long.toString(number).length(), 17);\r
- }\r
- String name = DirectoryManager.getTaskDirectory(ClustalW.class);\r
- assertTrue(name.startsWith(ClustalW.class.getSimpleName()));\r
- }\r
-\r
- /*\r
- * In fact the precision of System.nanoTime() varies depending on the JVM\r
- * Sun 1.6.0_17 JVM gives the same precision on linux x64 as on windows x32\r
- * but openjdk 1.6.x gives more digits on linux than sun JVM It looks like\r
- * the precision is desided at runtime, so the number of digits returned is\r
- * unknown\r
- */\r
- @Test(enabled = false)\r
- public void testNanoTime() {\r
- if (SysPrefs.isWindows) {\r
- assertEquals(Long.toString(System.nanoTime()).length(), 16);\r
- } else {\r
- // This is not always true for Linux\r
- assertEquals(Long.toString(System.nanoTime()).length(), 14);\r
- }\r
- }\r
-\r
-}\r
+++ /dev/null
-/* Copyright (c) 2009 Peter Troshin\r
- * \r
- * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0 \r
- * \r
- * This library is free software; you can redistribute it and/or modify it under the terms of the\r
- * Apache License version 2 as published by the Apache Software Foundation\r
- * \r
- * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
- * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
- * License for more details.\r
- * \r
- * A copy of the license is in apache_license.txt. It is also available here:\r
- * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
- * \r
- * Any republication or derived work distributed in source code form\r
- * must include this copyright and license notice.\r
- */\r
-\r
-package compbio.engine.conf;\r
-\r
-import static org.testng.Assert.assertNotNull;\r
-import static org.testng.Assert.assertTrue;\r
-\r
-import java.io.File;\r
-\r
-import org.testng.annotations.BeforeClass;\r
-import org.testng.annotations.Test;\r
-\r
-import compbio.metadata.AllTestSuit;\r
-import compbio.util.PropertyHelper;\r
-\r
-public class PropertyHelperManagerTester {\r
-\r
- PropertyHelper ph;\r
-\r
- @BeforeClass(alwaysRun=true)\r
- public void testLoadResources() {\r
- ph = PropertyHelperManager.getPropertyHelper();\r
- assertNotNull(ph);\r
- }\r
-\r
- @Test(groups = AllTestSuit.test_group_cluster)\r
- public void testClusterEngineConf() {\r
- // Below are the properties on cluster engine required for its\r
- // functioning\r
- validateDirProp("cluster.tmp.directory");\r
- }\r
-\r
- void validateDirProp(String propName) {\r
- assertNotNull(ph);\r
- assertNotNull(ph.getProperty(propName));\r
- File tmp = new File(ph.getProperty(propName).trim());\r
- assertTrue(tmp.exists());\r
- assertTrue(tmp.isDirectory());\r
- assertTrue(tmp.canRead());\r
- assertTrue(tmp.canWrite());\r
- }\r
-\r
- void validateExecFileProp(String propName) {\r
- validateFileProp(propName);\r
- File tmp = new File(ph.getProperty(propName));\r
- assertTrue(tmp.canExecute());\r
- }\r
-\r
- void validateFileProp(String propName) {\r
- assertNotNull(ph.getProperty(propName));\r
- File tmp = new File(ph.getProperty(propName));\r
- assertTrue(tmp.exists());\r
- assertTrue(tmp.isFile());\r
- assertTrue(tmp.canRead());\r
- }\r
-\r
- @Test\r
- public void validateClustalConfiguration() {\r
- // Below are the properties on Clustal executable required for its\r
- // functioning\r
- // Executables could not be verified as full path is constructed only at\r
- // runtime\r
- assertNotNull("local.clustalw.bin.windows");\r
- assertNotNull("local.clustalw.bin");\r
- assertNotNull("cluster.clustalw.bin");\r
- validateFileProp("clustalw.presets.file");\r
- validateFileProp("clustalw.parameters.file");\r
- //validateFileProp("clustalw.limits.file");\r
- }\r
-\r
- @Test\r
- public void validateMuscleConfiguration() {\r
- assertNotNull("local.muscle.bin.windows");\r
- assertNotNull("local.muscle.bin");\r
- assertNotNull("cluster.muscle.bin");\r
- validateFileProp("muscle.presets.file");\r
- validateFileProp("muscle.parameters.file");\r
- //validateFileProp("muscle.limits.file");\r
- }\r
-\r
- @Test\r
- public void validateTcoffeeConfiguration() {\r
- assertNotNull("local.tcoffee.bin.windows");\r
- assertNotNull("local.tcoffee.bin");\r
- assertNotNull("cluster.tcoffee.bin");\r
- validateFileProp("tcoffee.presets.file");\r
- validateFileProp("tcoffee.parameters.file");\r
- //validateFileProp("tcoffee.limits.file");\r
- }\r
-\r
- @Test\r
- public void validateMafftConfiguration() {\r
- assertNotNull("local.mafft.bin.windows");\r
- assertNotNull("local.mafft.bin");\r
- assertNotNull("cluster.mafft.bin");\r
- validateFileProp("mafft.presets.file");\r
- validateFileProp("mafft.parameters.file");\r
- //validateFileProp("mafft.limits.file");\r
- }\r
-}\r
+++ /dev/null
-/* Copyright (c) 2009 Peter Troshin\r
- * \r
- * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0 \r
- * \r
- * This library is free software; you can redistribute it and/or modify it under the terms of the\r
- * Apache License version 2 as published by the Apache Software Foundation\r
- * \r
- * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
- * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
- * License for more details.\r
- * \r
- * A copy of the license is in apache_license.txt. It is also available here:\r
- * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
- * \r
- * Any republication or derived work distributed in source code form\r
- * must include this copyright and license notice.\r
- */\r
-\r
-package compbio.engine.conf;\r
-\r
-import static org.testng.AssertJUnit.assertEquals;\r
-import static org.testng.AssertJUnit.assertFalse;\r
-import static org.testng.AssertJUnit.assertNotNull;\r
-import static org.testng.AssertJUnit.assertTrue;\r
-import static org.testng.AssertJUnit.fail;\r
-\r
-import java.io.ByteArrayOutputStream;\r
-import java.io.File;\r
-import java.io.FileInputStream;\r
-import java.io.FileNotFoundException;\r
-import java.io.FileOutputStream;\r
-import java.io.IOException;\r
-import java.net.MalformedURLException;\r
-import java.net.URL;\r
-import java.util.ArrayList;\r
-import java.util.List;\r
-\r
-import javax.xml.bind.JAXBException;\r
-import javax.xml.validation.Schema;\r
-import javax.xml.validation.Validator;\r
-\r
-import org.testng.annotations.BeforeMethod;\r
-import org.testng.annotations.Test;\r
-import org.xml.sax.SAXException;\r
-\r
-import compbio.metadata.AllTestSuit;\r
-import compbio.metadata.Option;\r
-import compbio.metadata.Parameter;\r
-import compbio.metadata.RunnerConfig;\r
-import compbio.metadata.ValueConstrain;\r
-import compbio.metadata.WrongParameterException;\r
-import compbio.runner.msa.Mafft;\r
-\r
-public class RunnerConfigMarshallerTester {\r
-\r
- public static String test_input = AllTestSuit.TEST_DATA_PATH_ABSOLUTE + "MafftParameters.xml";\r
- public static String test_schema_output = "RunnerConfigSchema.xml";\r
- public static String test_output = AllTestSuit.OUTPUT_DIR_ABSOLUTE + "MafftParameters.out.xml";\r
-\r
- public static String invalidDoc = AllTestSuit.TEST_DATA_PATH_ABSOLUTE + "InvalidMafftParameters.xml";\r
-\r
- RunnerConfig<Mafft> rconfig = null;\r
- Parameter<Mafft> matrixParam = null;\r
- RunnerConfigMarshaller<Mafft> pmarshaller = null;\r
-\r
- @BeforeMethod\r
- public void setup() {\r
- // write some parameters programmatically\r
- try {\r
- rconfig = new RunnerConfig<Mafft>();\r
- rconfig.setRunnerClassName(Mafft.class.getName());\r
- List<Option<Mafft>> prms = new ArrayList<Option<Mafft>>();\r
-\r
- Parameter<Mafft> p1 = new Parameter<Mafft>("Type", "Type of the sequence (PROTEIN or DNA)");\r
- // TODO publish help on a compbio web site\r
-\r
- p1.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");\r
- p1.addPossibleValues("PROTEIN", "DNA");\r
- p1.setOptionName("-TYPE");\r
- p1.setRequired(false);\r
-\r
- /*\r
- * -MATRIX= :Protein weight matrix=BLOSUM, PAM, GONNET, ID or\r
- * filename\r
- */\r
- Option<Mafft> p2 = new Option<Mafft>("MATRIX", "Protein weight matrix");\r
- // TODO publish help on a compbio web site\r
-\r
- p2.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");\r
-\r
- p2.addOptionNames("-jtree"); // "-retree"\r
- p2.setRequired(false);\r
-\r
- Parameter<Mafft> p3 = new Parameter<Mafft>("Matrix1", "Protein weight matrix");\r
- // TODO publish help on a compbio web site\r
- p3.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");\r
-\r
- p3.addPossibleValues("BLOSUM", "PAM", "GONNET", "ID");\r
- // This attribute is required by strict schema\r
- p3.setOptionName("--AAMATRIX");\r
- p3.setRequired(true);\r
- p3.setDefaultValue("pam");\r
- ValueConstrain vc = new ValueConstrain();\r
- vc.setType(ValueConstrain.Type.Float);\r
- vc.setMin("-10.12");\r
- vc.setMax("0");\r
- p3.setValidValue(vc);\r
-\r
- prms.add(p1);\r
- prms.add(p2);\r
- prms.add(p3);\r
- matrixParam = p3;\r
- rconfig.setOptions(prms);\r
-\r
- pmarshaller = new RunnerConfigMarshaller<Mafft>(RunnerConfig.class, Parameter.class, Option.class, ValueConstrain.class);\r
- } catch (JAXBException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (WrongParameterException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- }\r
-\r
- }\r
-\r
- @Test()\r
- public void testMarshalling() {\r
-\r
- File outfile = new File(this.test_output);\r
- try {\r
- pmarshaller.write(rconfig, new FileOutputStream(outfile));\r
- } catch (FileNotFoundException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (JAXBException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (IOException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- }\r
- assertTrue("Output file expected, but nothing found!", outfile.exists());\r
- outfile.delete();\r
- }\r
-\r
- @Test()\r
- public void testUnMarshalling() {\r
-\r
- File outfile = new File(this.test_output);\r
- try {\r
- pmarshaller.write(rconfig, new FileOutputStream(outfile));\r
-\r
- RunnerConfig<?> rconfig = pmarshaller.read(new FileInputStream(outfile), RunnerConfig.class, Parameter.class, Option.class,\r
- ValueConstrain.class);\r
- assertNotNull(rconfig);\r
- assertEquals(rconfig.getParameters().size(), this.rconfig.getParameters().size());\r
- assertEquals(rconfig.getRunnerClassName(), this.rconfig.getRunnerClassName());\r
- assertTrue(matrixParam.equals(rconfig.getArgument("MATRIX1")));\r
- assertFalse(matrixParam.equals(rconfig.getArgument("Type")));\r
- } catch (FileNotFoundException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (JAXBException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (IOException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- }\r
- // outfile.delete();\r
- }\r
-\r
- @Test()\r
- public void testValidation() {\r
- try {\r
- System.out.println("CCCC " + rconfig);\r
- // write schema\r
- pmarshaller.generateSchema(AllTestSuit.OUTPUT_DIR_ABSOLUTE, test_schema_output);\r
-\r
- File schemafile = new File(AllTestSuit.OUTPUT_DIR_ABSOLUTE, test_schema_output);\r
- assertTrue(schemafile.exists());\r
- // document is NOT valid even against a loose schema as elements in\r
- // java are annotated as required\r
- Validator looseValidator = RunnerConfigMarshaller.getValidator(schemafile.getAbsolutePath());\r
-\r
- // write output xml file\r
- File outfile = new File(this.test_output);\r
- pmarshaller.write(rconfig, new FileOutputStream(outfile));\r
-\r
- assertTrue("Invalid output is NOT expected", RunnerConfigMarshaller.validate(looseValidator, test_output));\r
-\r
- Schema strictSchema = RunnerConfigMarshaller.getSchema(AllTestSuit.TEST_DATA_PATH_ABSOLUTE + File.separator\r
- + "RunnerConfigSchema.xsd");\r
-\r
- Validator strictVal = RunnerConfigMarshaller.getValidator(strictSchema);\r
-\r
- // document is invalid against strict schema\r
- assertFalse("Invalid output is expected", RunnerConfigMarshaller.validate(strictVal, invalidDoc));\r
-\r
- // schemafile.delete();\r
- // outfile.delete();\r
-\r
- } catch (MalformedURLException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (JAXBException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (IOException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (SAXException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- }\r
-\r
- }\r
-\r
- @Test(expectedExceptions = JAXBException.class)\r
- public void testValidationOnMarshalling() throws SAXException, JAXBException, MalformedURLException {\r
- // This is not valid parameter\r
- Parameter<Mafft> p = new Parameter<Mafft>("MATRIXXX", "Protein weight matrix");\r
- // This attribute is required by strict schema\r
- // p.setOptionName("-M");\r
- p.setRequired(true);\r
- rconfig.addParameter(p);\r
- try {\r
-\r
- // strict schema invalidate this document and throw an exception\r
- // just discard the output\r
- pmarshaller.writeAndValidate(rconfig, AllTestSuit.TEST_DATA_PATH_ABSOLUTE + File.separator + "RunnerConfigSchema.xsd",\r
- new ByteArrayOutputStream());\r
-\r
- fail("Exception has been thrown before this place in unreachable");\r
-\r
- } catch (MalformedURLException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (IOException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- }\r
- }\r
-\r
- @Test()\r
- public void testSchemaFromCodeGeneration() {\r
- try {\r
-\r
- pmarshaller.generateSchema(AllTestSuit.OUTPUT_DIR_ABSOLUTE, test_schema_output);\r
- } catch (JAXBException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (IOException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- }\r
- File schemafile = new File(AllTestSuit.OUTPUT_DIR_ABSOLUTE, test_schema_output);\r
- assertTrue("Schema file expected but not found", schemafile.exists());\r
- assertTrue("Schema file seems to be empty", schemafile.length() > 50);\r
- // schemafile.delete();\r
- }\r
-\r
-}\r
+++ /dev/null
-/* Copyright (c) 2009 Peter Troshin\r
- * \r
- * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0 \r
- * \r
- * This library is free software; you can redistribute it and/or modify it under the terms of the\r
- * Apache License version 2 as published by the Apache Software Foundation\r
- * \r
- * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
- * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
- * License for more details.\r
- * \r
- * A copy of the license is in apache_license.txt. It is also available here:\r
- * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
- * \r
- * Any republication or derived work distributed in source code form\r
- * must include this copyright and license notice.\r
- */\r
-\r
-package compbio.engine.local;\r
-\r
-import static org.testng.Assert.assertEquals;\r
-import static org.testng.Assert.assertFalse;\r
-import static org.testng.Assert.assertNotNull;\r
-import static org.testng.Assert.assertNotSame;\r
-import static org.testng.Assert.assertTrue;\r
-import static org.testng.Assert.fail;\r
-\r
-import java.io.File;\r
-import java.util.concurrent.CancellationException;\r
-\r
-import org.testng.annotations.Test;\r
-\r
-import compbio.data.sequence.Alignment;\r
-import compbio.engine.AsyncExecutor;\r
-import compbio.engine.Configurator;\r
-import compbio.engine.client.ConfiguredExecutable;\r
-import compbio.engine.client.Executable;\r
-import compbio.engine.client.EngineUtil;\r
-import compbio.metadata.AllTestSuit;\r
-import compbio.metadata.JobStatus;\r
-import compbio.metadata.JobSubmissionException;\r
-import compbio.metadata.ResultNotAvailableException;\r
-import compbio.runner.msa.ClustalW;\r
-import compbio.runner.msa.Muscle;\r
-import compbio.util.SysPrefs;\r
-\r
-public class AsyncLocalRunnerTester {\r
-\r
- // Input path must be absolute to avoid coping input in working directory\r
- public static String unix_test_input = AllTestSuit.CURRENT_DIRECTORY\r
- + File.separator + AllTestSuit.TEST_DATA_PATH + "TO1381.fasta";\r
-\r
- public static String unix_test_AVG_input = AllTestSuit.CURRENT_DIRECTORY\r
- + File.separator + AllTestSuit.TEST_DATA_PATH\r
- + "50x500Protein.fasta";\r
-\r
- public static String unix_test_LARGE_input = AllTestSuit.CURRENT_DIRECTORY\r
- + File.separator + AllTestSuit.TEST_DATA_PATH\r
- + "200x500Protein.fasta";\r
-\r
- // Output file will be located in the task working directory, thus only name\r
- // is required\r
- public static String unix_test_outfile = "TO1381.alignment.out";\r
- public static String cluster_test_outfile = "TO1381.alignment.cluster.out";\r
-\r
- // Input path must be absolute to avoid coping input in working directory\r
- public static String win_test_input = AllTestSuit.CURRENT_DIRECTORY\r
- + File.separator + AllTestSuit.TEST_DATA_PATH + "TO1381.fasta";\r
-\r
- public static String win_test_LARGE_input = AllTestSuit.CURRENT_DIRECTORY\r
- + File.separator + AllTestSuit.TEST_DATA_PATH\r
- + "200x500Protein.fasta";\r
-\r
- public static String win_test_AVG_input = AllTestSuit.CURRENT_DIRECTORY\r
- + File.separator + AllTestSuit.TEST_DATA_PATH\r
- + "50x500Protein.fasta";\r
-\r
- // Output file will be located in the task working directory, thus only name\r
- // is required\r
- public static String win_test_outfile = "TO1381.alignment.out";\r
-\r
- @Test(expectedExceptions = { CancellationException.class,\r
- ResultNotAvailableException.class }, groups = { AllTestSuit.test_group_engine })\r
- public void testCancelLocally() throws ResultNotAvailableException {\r
- System.out.println("Running testCancelLocally");\r
- ClustalW clustal = new ClustalW();\r
-\r
- if (SysPrefs.isWindows) {\r
- System.out.println("Working in WINDOWS environment");\r
- clustal.setInput(win_test_input).setOutput(win_test_outfile);\r
- } else {\r
- System.out.println("Working in UNIX environment");\r
- clustal.setInput(unix_test_input).setOutput(unix_test_outfile);\r
- }\r
- AsyncExecutor lr = new AsyncLocalRunner();\r
- try {\r
- ConfiguredExecutable<ClustalW> confClust = Configurator\r
- .configureExecutable(clustal);\r
- String jobId = lr.submitJob(confClust);\r
- // Thread.sleep(10); //wait for 100ms\r
- assertNotSame(lr.getJobStatus(jobId), JobStatus.FINISHED,\r
- "Job has finished already. Too late to test cancel!");\r
- lr.cancelJob(jobId);\r
- // This call causes CancellationException to be thrown\r
- Executable<?> clustalr = lr.getResults(jobId);\r
- // @see AsyncLocalRunner.cleanup documents\r
- // assertTrue(lr.cleanup(jobId));\r
- } catch (JobSubmissionException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- }\r
- }\r
-\r
- @Test(invocationCount = 5, threadPoolSize = 4, groups = { AllTestSuit.test_group_engine })\r
- public void testSubmitLocally() {\r
- System.out.println("Running testSubmitLocally()");\r
- Muscle muscle = new Muscle();\r
-\r
- if (SysPrefs.isWindows) {\r
- System.out.println("Working in WINDOWS environment");\r
- muscle.setInput(win_test_input).setOutput(win_test_outfile);\r
- } else {\r
- System.out.println("Working in UNIX environment");\r
- muscle.setInput(unix_test_input).setOutput(unix_test_outfile);\r
- }\r
- AsyncExecutor lr = new AsyncLocalRunner();\r
- try {\r
- ConfiguredExecutable<Muscle> confMuscle = Configurator\r
- .configureExecutable(muscle);\r
- String jobId = lr.submitJob(confMuscle);\r
- // Thread.sleep(10); //wait for 100ms\r
- // assertNotSame("Job has finished already. Too late to test cancel!",\r
- // JobStatus.FINISHED, lr.getJobStatus(jobId));\r
- // This call causes CancellationException to be thrown\r
- Executable<?> muscler = lr.getResults(jobId);\r
- Alignment al = confMuscle.getResults();\r
- assertNotNull(al);\r
- } catch (JobSubmissionException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (ResultNotAvailableException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- }\r
- }\r
-\r
- @Test(invocationCount = 5, threadPoolSize = 4, groups = { AllTestSuit.test_group_engine })\r
- public void testGetStatus() {\r
- System.out.println("Running testGetStatus");\r
- Muscle muscle = new Muscle();\r
-\r
- if (SysPrefs.isWindows) {\r
- System.out.println("Working in WINDOWS environment");\r
- muscle.setInput(win_test_AVG_input).setOutput(win_test_outfile);\r
- } else {\r
- System.out.println("Working in UNIX environment");\r
- muscle.setInput(unix_test_AVG_input).setOutput(unix_test_outfile);\r
- }\r
- AsyncExecutor lr = new AsyncLocalRunner();\r
- try {\r
- ConfiguredExecutable<Muscle> confMuscle = Configurator\r
- .configureExecutable(muscle);\r
- String jobId = lr.submitJob(confMuscle);\r
- // Thread.sleep(10); //wait for 100ms\r
- JobStatus status = lr.getJobStatus(jobId);\r
- while (status == JobStatus.UNDEFINED) {\r
- assertTrue(status == JobStatus.UNDEFINED);\r
- Thread.sleep(100);\r
- status = lr.getJobStatus(jobId);\r
- }\r
- while (status != JobStatus.FINISHED) {\r
- Thread.sleep(500);\r
- assertTrue(status == JobStatus.RUNNING);\r
- status = lr.getJobStatus(jobId);\r
- }\r
- // assert that we get here, means that the job reached FINISHED\r
- // status\r
- // This call causes CancellationException to be thrown\r
- Executable<?> muscler = lr.getResults(jobId);\r
- /*\r
- * After results were obtained the task were removed for the queue,\r
- * and it status could not be determined\r
- */\r
- // Make sure list has been updated\r
- Thread.sleep(200);\r
- status = lr.getJobStatus(jobId);\r
- assertTrue(status == JobStatus.FINISHED);\r
-\r
- Alignment al = confMuscle.getResults();\r
-\r
- assertNotNull(al);\r
-\r
- } catch (JobSubmissionException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (InterruptedException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (ResultNotAvailableException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- }\r
- }\r
-\r
- @Test(expectedExceptions = CancellationException.class, groups = { AllTestSuit.test_group_engine })\r
- public void testMultipleCancelLocally() {\r
- System.out.println("Running testMultipleCancelLocally()");\r
- ClustalW clustal = new ClustalW();\r
- ClustalW clustal2 = new ClustalW();\r
- if (SysPrefs.isWindows) {\r
- System.out.println("Working in WINDOWS environment");\r
- clustal.setInput(win_test_input).setOutput(win_test_outfile);\r
- clustal2.setInput(win_test_input).setOutput(win_test_outfile);\r
- } else {\r
- System.out.println("Working in UNIX environment");\r
- clustal.setInput(unix_test_input).setOutput(unix_test_outfile);\r
- clustal2.setInput(unix_test_input).setOutput(unix_test_outfile);\r
- }\r
- try {\r
- ConfiguredExecutable<ClustalW> confClustal1 = Configurator\r
- .configureExecutable(clustal);\r
- ConfiguredExecutable<ClustalW> confClustal2 = Configurator\r
- .configureExecutable(clustal2);\r
- AsyncLocalRunner lr = new AsyncLocalRunner();\r
- AsyncLocalRunner lr2 = new AsyncLocalRunner();\r
-\r
- String jobId1 = lr.submitJob(confClustal1);\r
- String jobId2 = lr2.submitJob(confClustal2);\r
-\r
- // Thread.sleep(10); //wait for 100ms\r
- assertNotSame(lr.getJobStatus(jobId1), JobStatus.FINISHED,\r
- "Job has finished already. Too late to test cancel!");\r
- lr.cancelJob(jobId1);\r
- // Thread.sleep(10);\r
- assertNotSame(lr2.getJobStatus(jobId2), JobStatus.FINISHED,\r
- "Job has finished already. Too late to test cancel!");\r
- lr2.cancelJob(jobId2);\r
- // This call causes CancellationException to be thrown\r
- Executable<?> clustalr = lr.getResults(jobId1);\r
- Executable<?> clustalr2 = lr2.getResults(jobId2);\r
-\r
- assertTrue(lr.cleanup(jobId1));\r
- assertTrue(lr2.cleanup(jobId2));\r
-\r
- } catch (JobSubmissionException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (ResultNotAvailableException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- }\r
- }\r
-\r
- @Test(groups = { AllTestSuit.test_group_engine })\r
- public void testCancelCompletedTaskLocally() {\r
- System.out.println("Running testCancelCompletedTaskLocally");\r
- ClustalW clustal = new ClustalW();\r
- if (SysPrefs.isWindows) {\r
- System.out.println("Working in WINDOWS environment");\r
- clustal.setInput(win_test_input).setOutput(win_test_outfile);\r
- } else {\r
- System.out.println("Working in UNIX environment");\r
- clustal.setInput(unix_test_input).setOutput(unix_test_outfile);\r
- }\r
- try {\r
- ConfiguredExecutable<ClustalW> confClustal1 = Configurator\r
- .configureExecutable(clustal);\r
- AsyncLocalRunner lr = new AsyncLocalRunner();\r
- String jobId = lr.submitJob(confClustal1);\r
- Thread.currentThread();\r
- Thread.sleep(3000); // wait for 100ms\r
- assertEquals(lr.getJobStatus(jobId), JobStatus.FINISHED,\r
- "Job has not finished!");\r
- lr.cancelJob(jobId);\r
- // This call causes CancellationException to be thrown\r
- Executable<?> clustalr = lr.getResults(jobId);\r
- assertNotNull(clustalr);\r
-\r
- assertTrue(EngineUtil.isMarked(confClustal1.getWorkDirectory(),\r
- JobStatus.CANCELLED));\r
- assertTrue(EngineUtil.isMarked(confClustal1.getWorkDirectory(),\r
- JobStatus.STARTED));\r
- assertTrue(EngineUtil.isMarked(confClustal1.getWorkDirectory(),\r
- JobStatus.COLLECTED));\r
- assertTrue(EngineUtil.isMarked(confClustal1.getWorkDirectory(),\r
- JobStatus.FINISHED));\r
- assertFalse(EngineUtil.isMarked(confClustal1.getWorkDirectory(),\r
- JobStatus.SUBMITTED));\r
- } catch (JobSubmissionException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (InterruptedException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (ResultNotAvailableException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- }\r
- }\r
-\r
- @Test(groups = { AllTestSuit.test_group_engine })\r
- public void testAsyncRetrievOperation() {\r
- System.out.println("Running testAsyncOperation()");\r
- Muscle muscle = new Muscle();\r
-\r
- if (SysPrefs.isWindows) {\r
- System.out.println("Working in WINDOWS environment");\r
- muscle.setInput(win_test_input).setOutput(win_test_outfile);\r
- } else {\r
- System.out.println("Working in UNIX environment");\r
- muscle.setInput(unix_test_input).setOutput(unix_test_outfile);\r
- }\r
-\r
- try {\r
- ConfiguredExecutable<Muscle> confMuscle = Configurator\r
- .configureExecutable(muscle);\r
- AsyncExecutor lr = new AsyncLocalRunner();\r
- String jobId = lr.submitJob(confMuscle);\r
- AsyncLocalRunner as = new AsyncLocalRunner();\r
- ConfiguredExecutable<Muscle> muscler = (ConfiguredExecutable<Muscle>) as\r
- .getResults(jobId);\r
- assertNotNull(muscler);\r
- Alignment al1 = muscler.getResults();\r
-\r
- assertTrue(EngineUtil.isMarked(muscler.getWorkDirectory(),\r
- JobStatus.STARTED));\r
- assertTrue(EngineUtil.isMarked(muscler.getWorkDirectory(),\r
- JobStatus.COLLECTED));\r
- assertTrue(EngineUtil.isMarked(muscler.getWorkDirectory(),\r
- JobStatus.FINISHED));\r
- assertFalse(EngineUtil.isMarked(muscler.getWorkDirectory(),\r
- JobStatus.CANCELLED));\r
- assertFalse(EngineUtil.isMarked(muscler.getWorkDirectory(),\r
- JobStatus.SUBMITTED));\r
- Alignment al2 = confMuscle.getResults();\r
- assertNotNull(al1);\r
- assertNotNull(al2);\r
- assertTrue(al1.equals(al2));\r
- } catch (JobSubmissionException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (ResultNotAvailableException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- }\r
- }\r
-\r
- @Test(groups = { AllTestSuit.test_group_engine })\r
- public void testAsyncCancelOperation() {\r
- System.out.println("Running testAsyncOperation()");\r
- Muscle muscle = new Muscle();\r
-\r
- if (SysPrefs.isWindows) {\r
- System.out.println("Working in WINDOWS environment");\r
- muscle.setInput(win_test_input).setOutput(win_test_outfile);\r
- } else {\r
- System.out.println("Working in UNIX environment");\r
- muscle.setInput(unix_test_input).setOutput(unix_test_outfile);\r
- }\r
-\r
- try {\r
- ConfiguredExecutable<Muscle> confMuscle = Configurator\r
- .configureExecutable(muscle);\r
- AsyncExecutor lr = new AsyncLocalRunner();\r
- String jobId = lr.submitJob(confMuscle);\r
- // This call causes CancellationException to be thrown\r
- AsyncLocalRunner as = new AsyncLocalRunner();\r
- assertTrue(as.getJobStatus(jobId) != JobStatus.FINISHED);\r
- as.cancelJob(jobId);\r
- assertTrue(as.getJobStatus(jobId) == JobStatus.CANCELLED);\r
-\r
- assertTrue(EngineUtil.isMarked(confMuscle.getWorkDirectory(),\r
- JobStatus.CANCELLED));\r
- // could be both\r
- // assertFalse(Util.isMarked(confMuscle.getWorkDirectory(),\r
- // Util.StatFileType.STARTED));\r
- assertFalse(EngineUtil.isMarked(confMuscle.getWorkDirectory(),\r
- JobStatus.COLLECTED));\r
- assertFalse(EngineUtil.isMarked(confMuscle.getWorkDirectory(),\r
- JobStatus.FINISHED));\r
- assertFalse(EngineUtil.isMarked(confMuscle.getWorkDirectory(),\r
- JobStatus.SUBMITTED));\r
- // Executable<?> muscler = as.getResult(jobId);\r
- // assertNotNull(muscler);\r
- // Alignment al = muscle.getResults();\r
- // assertNotNull(al);\r
- } catch (JobSubmissionException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- }\r
- }\r
-}\r
+++ /dev/null
-/* Copyright (c) 2009 Peter Troshin\r
- * \r
- * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0 \r
- * \r
- * This library is free software; you can redistribute it and/or modify it under the terms of the\r
- * Apache License version 2 as published by the Apache Software Foundation\r
- * \r
- * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
- * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
- * License for more details.\r
- * \r
- * A copy of the license is in apache_license.txt. It is also available here:\r
- * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
- * \r
- * Any republication or derived work distributed in source code form\r
- * must include this copyright and license notice.\r
- */\r
-package compbio.engine.local;\r
-\r
-import static org.testng.Assert.assertEquals;\r
-import static org.testng.Assert.assertNotNull;\r
-import static org.testng.Assert.assertTrue;\r
-import static org.testng.Assert.fail;\r
-\r
-import java.util.ArrayList;\r
-import java.util.HashMap;\r
-import java.util.List;\r
-import java.util.Map;\r
-\r
-import org.testng.annotations.Test;\r
-\r
-import compbio.engine.AsyncExecutor;\r
-import compbio.engine.Configurator;\r
-import compbio.engine.SubmissionManager;\r
-import compbio.engine.client.ConfiguredExecutable;\r
-import compbio.engine.client.Executable;\r
-import compbio.metadata.AllTestSuit;\r
-import compbio.metadata.JobStatus;\r
-import compbio.metadata.JobSubmissionException;\r
-import compbio.metadata.ResultNotAvailableException;\r
-import compbio.runner.msa.ClustalW;\r
-import compbio.runner.msa.Muscle;\r
-\r
-public class EngineResourcesLeakTester {\r
-\r
- static int numberOfExecutions = 50;\r
-\r
- @Test(groups = { AllTestSuit.test_group_long })\r
- public void loadEngineRetrieveResultsManyTimes() {\r
-\r
- List<String> idlist = new ArrayList<String>();\r
- ClustalW clu = new ClustalW();\r
- clu.setInput(AllTestSuit.test_input_real);\r
- try {\r
- for (int i = 0; i < numberOfExecutions; i++) {\r
- ConfiguredExecutable<ClustalW> cclustal = Configurator\r
- .configureExecutable(clu, Executable.ExecProvider.Local);\r
- AsyncExecutor engine = Configurator.getAsyncEngine(cclustal);\r
- String jobId = engine.submitJob(cclustal);\r
- assertNotNull(jobId);\r
- Thread.sleep(50);\r
- assertNotNull(SubmissionManager.getTask(jobId));\r
- assertTrue(idlist.add(jobId));\r
- }\r
- } catch (JobSubmissionException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (InterruptedException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- }\r
-\r
- assertEquals(idlist.size(), numberOfExecutions);\r
- // assertEquals(SubmissionManager.submittedTasks.size(),\r
- // numberOfExecutions * 2);\r
-\r
- try {\r
- while (true) {\r
- int doneCounter = 0;\r
- for (String taskId : idlist) {\r
- AsyncExecutor engine = Configurator.getAsyncEngine(taskId);\r
- JobStatus status = engine.getJobStatus(taskId);\r
- System.out.println("Status for job: " + taskId + " "\r
- + status);\r
-\r
- if (status == JobStatus.FINISHED) {\r
- assertNotNull(taskId);\r
- System.out.println(taskId);\r
- // System.out.println(SubmissionManager.submittedTasks);\r
- // assertNotNull(SubmissionManager.getTask(taskId));\r
- Thread.sleep(200); // let buffers to be written\r
- ConfiguredExecutable<ClustalW> confclust = (ConfiguredExecutable<ClustalW>) engine\r
- .getResults(taskId);\r
- assertNotNull(confclust);\r
- assertNotNull(confclust.getResults());\r
- doneCounter++;\r
- }\r
- }\r
- if (doneCounter == numberOfExecutions) {\r
- break;\r
- }\r
- }\r
- } catch (ResultNotAvailableException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- } catch (InterruptedException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- }\r
- }\r
-\r
- @Test(groups = { AllTestSuit.test_group_long })\r
- public void loadEngineRetrieveResultsOnce() {\r
-\r
- Map<String, Boolean> idlist = new HashMap<String, Boolean>();\r
- Muscle muscle = new Muscle();\r
- muscle.setInput(AllTestSuit.test_input_real);\r
- muscle.setOutput("muscle.out");\r
- try {\r
- for (int i = 0; i < numberOfExecutions; i++) {\r
- ConfiguredExecutable<Muscle> cmuscle = Configurator\r
- .configureExecutable(muscle,\r
- Executable.ExecProvider.Local);\r
- AsyncExecutor engine = Configurator.getAsyncEngine(cmuscle);\r
- String jobId = engine.submitJob(cmuscle);\r
- assertNotNull(jobId);\r
- Thread.sleep(50);\r
- assertNotNull(SubmissionManager.getTask(jobId));\r
- assertTrue(idlist.put(jobId, false) == null);\r
- }\r
- } catch (JobSubmissionException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (InterruptedException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- }\r
-\r
- assertEquals(idlist.size(), numberOfExecutions);\r
- // assertEquals(SubmissionManager.submittedTasks.size(), 20);\r
-\r
- try {\r
- int doneCounter = 0;\r
- while (true) {\r
- if (doneCounter == numberOfExecutions) {\r
- break;\r
- }\r
- for (String taskId : idlist.keySet()) {\r
- Thread.sleep(50); // slow checking down\r
- AsyncExecutor engine = Configurator.getAsyncEngine(taskId);\r
- JobStatus status = engine.getJobStatus(taskId);\r
- System.out.println("Status for job: " + taskId + " "\r
- + status);\r
-\r
- if (status == JobStatus.FINISHED) {\r
- assertNotNull(taskId);\r
- if (idlist.get(taskId)) {\r
- continue;\r
- }\r
- System.out.println(taskId);\r
- // System.out.println(SubmissionManager.submittedTasks);\r
- // assertNotNull(SubmissionManager.getTask(taskId));\r
- Thread.sleep(100);// let the buffers to write things\r
- ConfiguredExecutable<ClustalW> confclust = (ConfiguredExecutable<ClustalW>) engine\r
- .getResults(taskId);\r
- assertNotNull(confclust);\r
- assertNotNull(confclust.getResults());\r
- idlist.put(taskId, true);\r
- doneCounter++;\r
- }\r
- }\r
- }\r
- } catch (ResultNotAvailableException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- } catch (InterruptedException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- }\r
- }\r
-}\r
+++ /dev/null
-/* Copyright (c) 2009 Peter Troshin\r
- * \r
- * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0 \r
- * \r
- * This library is free software; you can redistribute it and/or modify it under the terms of the\r
- * Apache License version 2 as published by the Apache Software Foundation\r
- * \r
- * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
- * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
- * License for more details.\r
- * \r
- * A copy of the license is in apache_license.txt. It is also available here:\r
- * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
- * \r
- * Any republication or derived work distributed in source code form\r
- * must include this copyright and license notice.\r
- */\r
-\r
-package compbio.engine.local;\r
-\r
-import static org.testng.Assert.assertFalse;\r
-import static org.testng.Assert.assertTrue;\r
-import static org.testng.AssertJUnit.assertNotSame;\r
-import static org.testng.AssertJUnit.assertNull;\r
-import static org.testng.AssertJUnit.fail;\r
-\r
-import java.util.concurrent.CancellationException;\r
-\r
-import org.testng.annotations.Test;\r
-\r
-import compbio.engine.Configurator;\r
-import compbio.engine.client.ConfiguredExecutable;\r
-import compbio.engine.client.Executable;\r
-import compbio.engine.client.EngineUtil;\r
-import compbio.metadata.AllTestSuit;\r
-import compbio.metadata.JobExecutionException;\r
-import compbio.metadata.JobStatus;\r
-import compbio.metadata.JobSubmissionException;\r
-import compbio.metadata.ResultNotAvailableException;\r
-import compbio.runner.msa.ClustalW;\r
-\r
-public class LocalRunnerTester {\r
-\r
- public static String cluster_test_outfile = "TO1381.clustal.cluster.out"; // "/homes/pvtroshin/TO1381.clustal.cluster.out\r
- // go up 2 directories from workspace: workspace/clustengine\r
- public static String test_input = AllTestSuit.TEST_DATA_PATH_ABSOLUTE\r
- + "TO1381.fasta";\r
- public static String test_outfile = "TO1381.clustal.out";\r
-\r
- @Test(expectedExceptions = CancellationException.class, groups = { AllTestSuit.test_group_engine })\r
- public void testCancelLocally() {\r
- ClustalW clustal = new ClustalW();\r
- clustal.setInput(test_input).setOutput(test_outfile);\r
-\r
- try {\r
- ConfiguredExecutable<ClustalW> confClust = Configurator\r
- .configureExecutable(clustal);\r
- LocalRunner lr = new LocalRunner(confClust);\r
-\r
- lr.executeJob();\r
- // Thread.sleep(10); //wait for 100ms\r
- assertNotSame("Job has finished already. Too late to test cancel!",\r
- JobStatus.FINISHED, lr.getJobStatus());\r
- lr.cancelJob();\r
- // This call causes CancellationException to be thrown\r
- Executable<?> clustalr = lr.waitForResult();\r
- assertTrue(EngineUtil.isMarked(confClust.getWorkDirectory(),\r
- JobStatus.CANCELLED));\r
- assertTrue(EngineUtil.isMarked(confClust.getWorkDirectory(),\r
- JobStatus.STARTED));\r
- assertTrue(EngineUtil.isMarked(confClust.getWorkDirectory(),\r
- JobStatus.COLLECTED));\r
- assertTrue(EngineUtil.isMarked(confClust.getWorkDirectory(),\r
- JobStatus.FINISHED));\r
- assertFalse(EngineUtil.isMarked(confClust.getWorkDirectory(),\r
- JobStatus.SUBMITTED));\r
- } catch (JobSubmissionException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (JobExecutionException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- }\r
- }\r
-\r
- @Test(expectedExceptions = { CancellationException.class,\r
- JobExecutionException.class }, groups = { AllTestSuit.test_group_engine })\r
- public void testMultipleCancelLocally() throws JobExecutionException {\r
- ClustalW clustal = new ClustalW();\r
- ClustalW clustal2 = new ClustalW();\r
- clustal.setInput(test_input).setOutput(test_outfile);\r
- clustal2.setInput(test_input).setOutput(test_outfile);\r
- try {\r
- ConfiguredExecutable<ClustalW> confClust = Configurator\r
- .configureExecutable(clustal);\r
- ConfiguredExecutable<ClustalW> confClust2 = Configurator\r
- .configureExecutable(clustal2);\r
-\r
- LocalRunner lr = new LocalRunner(confClust);\r
- LocalRunner lr2 = new LocalRunner(confClust2);\r
-\r
- lr.executeJob();\r
- lr2.executeJob();\r
-\r
- // Thread.sleep(10); //wait for 100ms\r
- assertNotSame("Job has finished already. Too late to test cancel!",\r
- JobStatus.FINISHED, lr.getJobStatus());\r
- lr.cancelJob();\r
- // Thread.sleep(10);\r
- assertNotSame("Job has finished already. Too late to test cancel!",\r
- JobStatus.FINISHED, lr2.getJobStatus());\r
- lr2.cancelJob();\r
- // This call causes CancellationException to be thrown\r
- Executable<?> clustalr = lr.waitForResult();\r
- Executable<?> clustalr2 = lr2.waitForResult();\r
-\r
- } catch (JobSubmissionException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- }\r
- }\r
-\r
- @Test(expectedExceptions = { CancellationException.class }, groups = { AllTestSuit.test_group_engine })\r
- public void testCancelCompletedTaskLocally() throws JobExecutionException {\r
- ClustalW clustal = new ClustalW();\r
- clustal.setInput(test_input).setOutput(test_outfile);\r
-\r
- try {\r
- ConfiguredExecutable<ClustalW> confClust = Configurator\r
- .configureExecutable(clustal, Executable.ExecProvider.Local);\r
- LocalRunner lr = new LocalRunner(confClust);\r
- lr.executeJob();\r
- Thread.currentThread();\r
- Thread.sleep(30); // wait for 100ms\r
- assertNotSame("Job has not finished!", JobStatus.FINISHED, lr\r
- .getJobStatus());\r
- lr.cancelJob();\r
- // This call causes ResultNotAvailableException to be thrown\r
- ConfiguredExecutable<?> clustalr = lr.waitForResult();\r
- assertNull(clustalr.getResults());\r
- } catch (JobSubmissionException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (InterruptedException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (ResultNotAvailableException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- }\r
- }\r
-\r
-}\r
+++ /dev/null
-/* Copyright (c) 2009 Peter Troshin\r
- * Copyright (c) 2013 Alexander Sherstnev\r
- * \r
- * JAva Bioinformatics Analysis Web Services (JABAWS)\r
- * @version: 2.5 \r
- * \r
- * This library is free software; you can redistribute it and/or modify it under the terms of the\r
- * Apache License version 2 as published by the Apache Software Foundation\r
- * \r
- * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
- * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
- * License for more details.\r
- * \r
- * A copy of the license is in apache_license.txt. It is also available here:\r
- * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
- * \r
- * Any republication or derived work distributed in source code form\r
- * must include this copyright and license notice.\r
- */\r
-\r
-package compbio.metadata;\r
-\r
-import java.io.File;\r
-import compbio.util.SysPrefs;\r
-\r
-public class AllTestSuit {\r
- public final static String test_group_cluster = "cluster";\r
- public final static String test_group_runner = "runner";\r
- public final static String test_group_non_windows = "non_windows";\r
- public final static String test_group_windows_only = "windows_only";\r
- public final static String test_group_engine = "engine";\r
- public final static String test_group_long = "performance";\r
- public final static String test_group_webservices = "webservices";\r
-\r
- // For this to work execution must start from the project directory!\r
- public static final String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory() + File.separator;\r
- public static final String TEST_DATA_PATH = "testsrc" + File.separator + "testdata" + File.separator;\r
- public static final String TEST_DATA_PATH_ABSOLUTE = AllTestSuit.CURRENT_DIRECTORY + TEST_DATA_PATH;\r
-\r
- // For cluster execution paths MUST BE ABSOLUTE as cluster hosts will not be\r
- // able to access the task otherwise\r
- public static final String OUTPUT_DIR_ABSOLUTE = AllTestSuit.CURRENT_DIRECTORY + "local_jobsout" + File.separator;\r
- public static final String RUNNER_TEST_LOGGER = "RunnerLogger";\r
-\r
- public static final String test_input = AllTestSuit.TEST_DATA_PATH_ABSOLUTE + "TO1381.fasta";\r
- public static final String test_alignment_input = AllTestSuit.TEST_DATA_PATH_ABSOLUTE + "TO1381.fasta.aln";\r
- public static final String test_input_real = AllTestSuit.TEST_DATA_PATH_ABSOLUTE + "50x500Protein.fasta";\r
- public static final String test_input_dna = AllTestSuit.TEST_DATA_PATH_ABSOLUTE + "3dnaseqs.fasta";\r
- public static final String test_input_large = AllTestSuit.TEST_DATA_PATH_ABSOLUTE + "1000x3000Dna.fasta";\r
- \r
- public static final String test_input_aln = AllTestSuit.TEST_DATA_PATH_ABSOLUTE + "unfolded_RF00031.aln";\r
-\r
-}\r
+++ /dev/null
-/* Copyright (c) 2009 Peter Troshin\r
- * \r
- * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0 \r
- * \r
- * This library is free software; you can redistribute it and/or modify it under the terms of the\r
- * Apache License version 2 as published by the Apache Software Foundation\r
- * \r
- * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
- * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
- * License for more details.\r
- * \r
- * A copy of the license is in apache_license.txt. It is also available here:\r
- * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
- * \r
- * Any republication or derived work distributed in source code form\r
- * must include this copyright and license notice.\r
- */\r
-\r
-package compbio.metadata;\r
-\r
-import static org.testng.Assert.fail;\r
-\r
-import java.io.File;\r
-import java.io.FileInputStream;\r
-import java.io.FileNotFoundException;\r
-\r
-import javax.xml.bind.JAXBException;\r
-\r
-import org.testng.annotations.BeforeMethod;\r
-import org.testng.annotations.Test;\r
-\r
-import compbio.engine.conf.RunnerConfigMarshaller;\r
-import compbio.metadata.RunnerConfig;\r
-import compbio.runner.OptionCombinator;\r
-import compbio.runner.msa.ClustalW;\r
-import compbio.runner.msa.Mafft;\r
-import compbio.runner.msa.Muscle;\r
-\r
-public class OptionCombinatorTester {\r
-\r
- static final String mafftConfigFile = AllTestSuit.TEST_DATA_PATH\r
- + "MafftParameters.xml";\r
-\r
- static final String muscleConfigFile = AllTestSuit.TEST_DATA_PATH\r
- + "MuscleParameters.xml";\r
-\r
- static final String clustalConfigFile = AllTestSuit.TEST_DATA_PATH\r
- + "ClustalParameters.xml";\r
-\r
- RunnerConfig<Mafft> mafftConfig = null;\r
- RunnerConfig<Mafft> muscleConfig = null;\r
- RunnerConfig<Mafft> clustalConfig = null;\r
-\r
- @BeforeMethod\r
- @SuppressWarnings("unchecked")\r
- void setup() {\r
- try {\r
- RunnerConfigMarshaller<Mafft> mf = new RunnerConfigMarshaller<Mafft>(\r
- RunnerConfig.class);\r
- mafftConfig = mf.read(\r
- new FileInputStream(new File(mafftConfigFile)),\r
- RunnerConfig.class);\r
- RunnerConfigMarshaller<Muscle> musclemarsh = new RunnerConfigMarshaller<Muscle>(\r
- RunnerConfig.class);\r
- muscleConfig = musclemarsh.read(new FileInputStream(new File(\r
- muscleConfigFile)), RunnerConfig.class);\r
-\r
- RunnerConfigMarshaller<ClustalW> clustalmarsh = new RunnerConfigMarshaller<ClustalW>(\r
- RunnerConfig.class);\r
- clustalConfig = clustalmarsh.read(new FileInputStream(new File(\r
- clustalConfigFile)), RunnerConfig.class);\r
-\r
- } catch (FileNotFoundException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- } catch (JAXBException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- }\r
- }\r
-\r
- @Test\r
- public void testgetAllOptions() {\r
- OptionCombinator opc = new OptionCombinator(mafftConfig);\r
- System.out.println(opc.getOptionsAtRandom());\r
- OptionCombinator muscleOpc = new OptionCombinator(muscleConfig);\r
- System.out.println("Mucle " + muscleOpc.getOptionsAtRandom());\r
- OptionCombinator clustalOpc = new OptionCombinator(clustalConfig);\r
- System.out.println("Clustal " + clustalOpc.getOptionsAtRandom());\r
-\r
- }\r
-\r
- @Test\r
- public void testgetAllParameters() {\r
- OptionCombinator opc = new OptionCombinator(mafftConfig);\r
- System.out.println(opc.getAllParameters());\r
- OptionCombinator muscleOpc = new OptionCombinator(muscleConfig);\r
- System.out.println("Muscle : " + muscleOpc.getAllParameters());\r
- OptionCombinator clustalOpc = new OptionCombinator(clustalConfig);\r
- System.out.println("Clustal : " + clustalOpc.getAllParameters());\r
- }\r
-}\r
+++ /dev/null
-/* Copyright (c) 2009 Peter Troshin\r
- * \r
- * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0 \r
- * \r
- * This library is free software; you can redistribute it and/or modify it under the terms of the\r
- * Apache License version 2 as published by the Apache Software Foundation\r
- * \r
- * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
- * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
- * License for more details.\r
- * \r
- * A copy of the license is in apache_license.txt. It is also available here:\r
- * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
- * \r
- * Any republication or derived work distributed in source code form\r
- * must include this copyright and license notice.\r
- */\r
-\r
-package compbio.metadata;\r
-\r
-import static org.testng.AssertJUnit.assertEquals;\r
-import static org.testng.AssertJUnit.assertFalse;\r
-import static org.testng.AssertJUnit.assertNotNull;\r
-import static org.testng.AssertJUnit.assertTrue;\r
-import static org.testng.AssertJUnit.fail;\r
-\r
-import java.io.File;\r
-import java.io.FileInputStream;\r
-import java.io.FileNotFoundException;\r
-import java.io.FileOutputStream;\r
-import java.io.IOException;\r
-import java.net.MalformedURLException;\r
-import java.net.URL;\r
-import java.util.ArrayList;\r
-import java.util.List;\r
-\r
-import javax.xml.bind.JAXBContext;\r
-import javax.xml.bind.JAXBElement;\r
-import javax.xml.bind.JAXBException;\r
-import javax.xml.bind.Unmarshaller;\r
-import javax.xml.transform.stream.StreamSource;\r
-\r
-import org.testng.annotations.BeforeMethod;\r
-import org.testng.annotations.Test;\r
-import org.xml.sax.SAXException;\r
-\r
-import compbio.engine.conf.RunnerConfigMarshaller;\r
-import compbio.runner.msa.Mafft;\r
-\r
-public class OptionMarshallerTester {\r
-\r
- public static String test_input = AllTestSuit.TEST_DATA_PATH_ABSOLUTE + "MafftParameters.xml";\r
- public static String test_schema_output = "NextGenMafftOptionsSchema.xml";\r
- public static String test_output = "MafftOptions.xml.out";\r
- public static String reWrittenInput = AllTestSuit.OUTPUT_DIR_ABSOLUTE + "rewrittenMafftParams.xml";\r
-\r
- RunnerConfig<Mafft> rconfig = null;\r
- Option<Mafft> matrixParam = null;\r
-\r
- @BeforeMethod()\r
- public void setup() {\r
- // write some parameters programmatically\r
- try {\r
- rconfig = new RunnerConfig<Mafft>();\r
- rconfig.setRunnerClassName(Mafft.class.getName());\r
- List<Option<Mafft>> prms = new ArrayList<Option<Mafft>>();\r
-\r
- Parameter<Mafft> p1 = new Parameter<Mafft>("Type", "Type of the sequence (PROTEIN or DNA)");\r
- // TODO publish help on a compbio web site\r
-\r
- p1.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");\r
- p1.addPossibleValues("PROTEIN", "DNA");\r
- p1.setOptionName("-TYPE");\r
- p1.setRequired(false);\r
-\r
- /*\r
- * -MATRIX= :Protein weight matrix=BLOSUM, PAM, GONNET, ID or\r
- * filename\r
- */\r
- Option<Mafft> p2 = new Option<Mafft>("MATRIX", "Protein weight matrix");\r
- // TODO publish help on a compbio web site\r
-\r
- p2.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");\r
-\r
- p2.addOptionNames("-jtree");\r
- p2.addOptionNames("-jfasta");\r
- p2.setRequired(false);\r
-\r
- Parameter<Mafft> p3 = new Parameter<Mafft>("MATRIX2", "Protein weight matrix");\r
- // TODO publish help on a compbio web site\r
- p3.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");\r
-\r
- p3.addPossibleValues("BLOSUM", "PAM", "GONNET", "ID");\r
- // This attribute is required by strict schema\r
- p3.setOptionName("-MATRIX");\r
- p3.setRequired(true);\r
- p3.setDefaultValue("id");\r
- ValueConstrain vc = new ValueConstrain();\r
- vc.setType(ValueConstrain.Type.Float);\r
- vc.setMin("-10.12");\r
- vc.setMax("0");\r
- p3.setValidValue(vc);\r
-\r
- prms.add(p1);\r
- prms.add(p2);\r
- prms.add(p3);\r
- matrixParam = p2;\r
- rconfig.setOptions(prms);\r
-\r
- } catch (WrongParameterException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- }\r
- }\r
-\r
- @Test(expectedExceptions = { javax.xml.bind.MarshalException.class })\r
- public void testMarshalling() throws JAXBException {\r
-\r
- File outfile = new File(AllTestSuit.OUTPUT_DIR_ABSOLUTE, test_output);\r
- try {\r
- RunnerConfigMarshaller<Mafft> rmarsh = new RunnerConfigMarshaller<Mafft>(RunnerConfig.class);\r
-\r
- // This throws an exception\r
- // I am not sure why\r
- rmarsh.writeAndValidate(rconfig, AllTestSuit.TEST_DATA_PATH_ABSOLUTE + File.separator + "RunnerConfigSchema.xsd",\r
- new FileOutputStream(outfile));\r
-\r
- } catch (FileNotFoundException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (IOException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (SAXException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- }\r
- assertTrue("Output file expected, but nothing found!", outfile.exists());\r
- // outfile.delete();\r
- }\r
-\r
- @Test()\r
- public void testUnMarshalling() {\r
- try {\r
- File input = new File(this.test_input);\r
- assertTrue(input.exists());\r
- JAXBContext ctx = JAXBContext.newInstance(RunnerConfig.class);\r
- Unmarshaller um = ctx.createUnmarshaller();\r
- JAXBElement<RunnerConfig> rconfig = um.unmarshal(new StreamSource(input), RunnerConfig.class);\r
- RunnerConfig<Mafft> runner = rconfig.getValue();\r
- assertNotNull(runner);\r
- System.out.println(runner);\r
- assertFalse(runner.options.isEmpty());\r
- assertFalse(runner.parameters.isEmpty());\r
- assertEquals(7, runner.options.size());\r
- assertEquals(8, runner.parameters.size());\r
- Option<Mafft> stypeOption = runner.getArgument("Sequence type");\r
- System.out.println(stypeOption);\r
- assertNotNull(stypeOption);\r
- assertFalse(stypeOption.isRequired);\r
- assertEquals("--auto", stypeOption.defaultValue);\r
- assertEquals(2, stypeOption.optionNames.size());\r
-\r
- assertEquals(" ", runner.getPrmSeparator());\r
- Option<Mafft> guidetrOption = runner.getArgument("Guide tree rebuild");\r
- Parameter<Mafft> guidetr = (Parameter<Mafft>) guidetrOption;\r
- ValueConstrain constraint = guidetr.getValidValue();\r
- assertEquals("Integer", constraint.type.toString());\r
- assertEquals(1, constraint.getMin());\r
- assertEquals(100, constraint.getMax());\r
-\r
- RunnerConfigMarshaller<Mafft> rmarsh = new RunnerConfigMarshaller<Mafft>(RunnerConfig.class);\r
- // Now see if we can write a valid document back discard the actual\r
- // output only validation is important here\r
- rmarsh.write(rconfig, new FileOutputStream(new File(reWrittenInput)));\r
- RunnerConfig<Mafft> rc = rmarsh.readAndValidate(new FileInputStream(new File(reWrittenInput)), RunnerConfig.class);\r
- assertEquals(runner, rc);\r
-\r
- } catch (JAXBException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (IOException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (SAXException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- }\r
- }\r
-}\r
+++ /dev/null
-/* Copyright (c) 2009 Peter Troshin\r
- * \r
- * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0 \r
- * \r
- * This library is free software; you can redistribute it and/or modify it under the terms of the\r
- * Apache License version 2 as published by the Apache Software Foundation\r
- * \r
- * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
- * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
- * License for more details.\r
- * \r
- * A copy of the license is in apache_license.txt. It is also available here:\r
- * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
- * \r
- * Any republication or derived work distributed in source code form\r
- * must include this copyright and license notice.\r
- */\r
-\r
-package compbio.metadata;\r
-\r
-import static org.testng.Assert.assertEquals;\r
-import static org.testng.Assert.assertFalse;\r
-import static org.testng.Assert.assertNotNull;\r
-import static org.testng.Assert.assertTrue;\r
-import static org.testng.Assert.fail;\r
-\r
-import java.io.File;\r
-import java.io.FileInputStream;\r
-import java.io.FileNotFoundException;\r
-import java.io.IOException;\r
-import java.util.ArrayList;\r
-import java.util.Collections;\r
-import java.util.List;\r
-\r
-import javax.xml.bind.JAXBContext;\r
-import javax.xml.bind.JAXBElement;\r
-import javax.xml.bind.JAXBException;\r
-import javax.xml.bind.Unmarshaller;\r
-import javax.xml.transform.stream.StreamSource;\r
-\r
-import org.testng.annotations.BeforeTest;\r
-import org.testng.annotations.Test;\r
-import org.xml.sax.SAXException;\r
-\r
-import compbio.engine.conf.RunnerConfigMarshaller;\r
-import compbio.runner.msa.Mafft;\r
-\r
-public class PresetTester {\r
-\r
- public static final String input = AllTestSuit.TEST_DATA_PATH\r
- + "MafftPresets.xml";\r
- public static String test_input = AllTestSuit.TEST_DATA_PATH_ABSOLUTE\r
- + "MafftParameters.xml";\r
-\r
- PresetManager<Mafft> presets = null;\r
- RunnerConfig<Mafft> rconfParams = null;\r
-\r
- @BeforeTest(enabled = true)\r
- public void loadPresets() {\r
- try {\r
- // Load Preset definitions\r
- RunnerConfigMarshaller<Mafft> rconfigPresets = new RunnerConfigMarshaller<Mafft>(\r
- PresetManager.class);\r
- File infile = new File(input);\r
- assertTrue(infile.exists());\r
- presets = rconfigPresets.read(new FileInputStream(infile),\r
- PresetManager.class);\r
- assertNotNull(presets);\r
- assertFalse(presets.preset.isEmpty());\r
-\r
- // Load Parameters definitions\r
- File input = new File(this.test_input);\r
- assertTrue(input.exists());\r
- JAXBContext ctx = JAXBContext.newInstance(RunnerConfig.class);\r
- Unmarshaller um = ctx.createUnmarshaller();\r
- JAXBElement<RunnerConfig> rconfigParams = um.unmarshal(\r
- new StreamSource(input), RunnerConfig.class);\r
- rconfParams = rconfigParams.getValue();\r
- assertNotNull(rconfParams);\r
-\r
- } catch (JAXBException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- } catch (FileNotFoundException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- }\r
- }\r
-\r
- @Test\r
- public void marshallPreset() {\r
- try {\r
- RunnerConfigMarshaller<Mafft> rconfig = new RunnerConfigMarshaller<Mafft>(\r
- PresetManager.class);\r
- PresetManager<Mafft> pman = getPresets();\r
- assertNotNull(pman);\r
- rconfig.readAndValidate(new FileInputStream(new File(input)),\r
- PresetManager.class);\r
- } catch (JAXBException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- } catch (IOException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- } catch (SAXException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- }\r
- }\r
-\r
- @Test\r
- public void validatePresets() {\r
- assertNotNull(presets);\r
- assertEquals(presets.getPresets().size(), 6);\r
- try {\r
- for (Preset<Mafft> pr : presets.getPresets()) {\r
- List<Option<Mafft>> options;\r
- options = pr.getArguments(rconfParams);\r
- assertFalse(options.isEmpty());\r
- if (pr.name.equals("L-INS-i (Accuracy-oriented)")) {\r
- assertEquals(options.size(), 2);\r
- Option<Mafft> o = options.get(0);\r
- if (o.name.equals("Pairwise alignment computation method")) {\r
- List<String> onames = o.getOptionNames();\r
- boolean match = false;\r
- for (String oname : onames) {\r
- if (oname.equals("--localpair")) {\r
- match = true;\r
- break;\r
- }\r
- }\r
- assertTrue(match);\r
- }\r
- }\r
- if (pr.name.equals("NW-NS-PartTree-1 (Speed oriented)")) {\r
- assertEquals(options.size(), 4);\r
- }\r
- }\r
- } catch (WrongParameterException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- }\r
- }\r
-\r
- @Test\r
- public void testPresetWithMuptiOptions() {\r
- assertNotNull(presets);\r
- assertEquals(presets.getPresets().size(), 6);\r
- try {\r
- for (Preset<Mafft> pr : presets.getPresets()) {\r
- List<Option<Mafft>> options;\r
- options = pr.getArguments(rconfParams);\r
- assertFalse(options.isEmpty());\r
- if (pr.name.equals("E-INS-i (Accuracy-oriented)")) {\r
- assertEquals(options.size(), 3);\r
- Option<Mafft> o = options.get(0);\r
- if (o.name.equals("Pairwise alignment computation method")) {\r
- List<String> onames = o.getOptionNames();\r
- boolean match = false;\r
- for (String oname : onames) {\r
- if (oname.equals("--genafpair")) {\r
- match = true;\r
- break;\r
- }\r
- }\r
- assertTrue(match);\r
- }\r
- }\r
- if (pr.name.equals("NW-NS-PartTree-1 (Speed oriented)")) {\r
- assertEquals(options.size(), 4);\r
- }\r
- }\r
- } catch (WrongParameterException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- }\r
- }\r
-\r
- private static PresetManager<Mafft> getPresets() {\r
- Preset<Mafft> preset1 = new Preset<Mafft>();\r
- preset1.name = "L-INS-i (Accuracy-oriented)";\r
- preset1.description = "dsfjkg fdjksghkjsgdfh jksdfg sdfgkjhsdfgk kjsdfg ";\r
-\r
- List<String> optionNames = new ArrayList<String>();\r
- optionNames.add("--localpair");\r
- optionNames.add("--maxiterate 1000");\r
- preset1.option = optionNames;\r
- PresetManager<Mafft> prman = new PresetManager<Mafft>();\r
- prman.preset = Collections.singletonList(preset1);\r
- prman.runnerClassName = Mafft.class.getCanonicalName();\r
-\r
- return prman;\r
- }\r
-}\r
+++ /dev/null
-/* Copyright (c) 2009 Peter Troshin\r
- * \r
- * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0 \r
- * \r
- * This library is free software; you can redistribute it and/or modify it under the terms of the\r
- * Apache License version 2 as published by the Apache Software Foundation\r
- * \r
- * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
- * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
- * License for more details.\r
- * \r
- * A copy of the license is in apache_license.txt. It is also available here:\r
- * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
- * \r
- * Any republication or derived work distributed in source code form\r
- * must include this copyright and license notice.\r
- */\r
-package compbio.metadata;\r
-\r
-import static org.testng.AssertJUnit.assertEquals;\r
-import static org.testng.AssertJUnit.assertFalse;\r
-import static org.testng.AssertJUnit.assertTrue;\r
-import static org.testng.AssertJUnit.fail;\r
-\r
-import java.net.MalformedURLException;\r
-import java.net.URL;\r
-import java.util.ArrayList;\r
-import java.util.Arrays;\r
-import java.util.HashSet;\r
-import java.util.List;\r
-\r
-import javax.xml.bind.JAXBException;\r
-import javax.xml.bind.ValidationException;\r
-\r
-import org.testng.annotations.BeforeMethod;\r
-import org.testng.annotations.Test;\r
-\r
-import compbio.engine.conf.RunnerConfigMarshaller;\r
-import compbio.runner.msa.Mafft;\r
-\r
-public class RunnerConfigTester {\r
-\r
- public static String test_input = AllTestSuit.TEST_DATA_PATH_ABSOLUTE + "MafftParameters.xml";\r
-\r
- RunnerConfig<Mafft> rconfig = null;\r
-\r
- @BeforeMethod\r
- public void setup() {\r
- try {\r
- rconfig = new RunnerConfig<Mafft>();\r
- rconfig.setRunnerClassName(Mafft.class.getName());\r
- List<Option<Mafft>> prms = new ArrayList<Option<Mafft>>();\r
-\r
- RunnerConfigMarshaller<Mafft> pmarshaller = new RunnerConfigMarshaller<Mafft>(RunnerConfig.class, Parameter.class,\r
- Option.class, ValueConstrain.class);\r
- } catch (JAXBException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- }\r
- }\r
-\r
- @Test\r
- public void testValidate() {\r
- try {\r
- rconfig.validate();\r
- } catch (ValidationException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (IllegalStateException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- }\r
- }\r
-\r
- @Test(expectedExceptions = WrongParameterException.class)\r
- public void testCreateParameter() throws WrongParameterException {\r
- Parameter<Mafft> p3 = new Parameter<Mafft>("Matrix1", "Protein weight matrix");\r
- // TODO publish help on a compbio web site\r
- p3.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");\r
-\r
- p3.addPossibleValues("BLOSUM", "PAM", "GONNET", "ID");\r
- // This attribute is required by strict schema\r
- p3.setOptionName("--AAMATRIX");\r
- p3.setRequired(true);\r
- // THIS LINE IS CAUSING EXCEPTION AS DEFAULT VALUE MUST BE DEFINED\r
- // IN WITHIN POSSIBLE VALUES\r
- p3.setDefaultValue("pam22");\r
- String com = p3.toCommand(" ");\r
- System.out.println("AAAAAAAAAAAAAA!" + com);\r
- }\r
-\r
- @Test()\r
- public void testParameterToCommand() throws WrongParameterException {\r
- Parameter<Mafft> p3 = new Parameter<Mafft>("Matrix1", "Protein weight matrix");\r
- // TODO publish help on a compbio web site\r
- p3.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");\r
-\r
- p3.addPossibleValues("BLOSUM", "PAM", "GONNET", "ID");\r
- // This attribute is required by strict schema\r
- p3.setOptionName("--AAMATRIX");\r
- p3.setRequired(true);\r
- // THIS LINE IS CAUSING EXCEPTION AS DEFAULT VALUE MUST BE DEFINED\r
- // IN WITHIN POSSIBLE VALUES\r
- p3.setDefaultValue("PAM");\r
- String com = p3.toCommand("=");\r
- assertTrue(com.startsWith("--AAMATRIX"));\r
- assertTrue(com.endsWith("PAM"));\r
- assertTrue(com.contains("="));\r
- p3.setDefaultValue("ID");\r
- com = p3.toCommand("=");\r
- assertFalse(com.endsWith("PAM"));\r
- assertFalse(com.contains("PAM"));\r
- }\r
-\r
- @Test(expectedExceptions = ValidationException.class)\r
- public void testOptionNoDefaultValidate() throws ValidationException {\r
- Option<Mafft> p3 = new Option<Mafft>("Matrix1", "Protein weight matrix");\r
- // TODO publish help on a compbio web site\r
- p3.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");\r
-\r
- p3.setOptionNames(new HashSet(Arrays.asList("--AAMATRIX", "--ABMAT", "--BBBB")));\r
- p3.setRequired(true);\r
- // THIS LINE IS CAUSING EXCEPTION AS DEFAULT VALUE MUST BE DEFINED\r
- // IN WITHIN POSSIBLE VALUES\r
- p3.validate();\r
- }\r
-\r
- @Test(expectedExceptions = WrongParameterException.class)\r
- public void testOptionSetInvalidValue() throws WrongParameterException {\r
-\r
- Option<Mafft> p3 = new Option<Mafft>("Matrix1", "Protein weight matrix");\r
- // TODO publish help on a compbio web site\r
- p3.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");\r
-\r
- p3.setOptionNames(new HashSet(Arrays.asList("--AAMATRIX", "--ABMAT", "--BBBB")));\r
- p3.setRequired(true);\r
- // THIS LINE IS CAUSING EXCEPTION AS DEFAULT VALUE MUST BE DEFINED\r
- // IN WITHIN POSSIBLE VALUES\r
- p3.setDefaultValue("AAA");\r
- }\r
-\r
- @Test()\r
- public void testOptionToCommand() {\r
- try {\r
- Option<Mafft> p3 = new Option<Mafft>("Matrix1", "Protein weight matrix");\r
- // TODO publish help on a compbio web site\r
- p3.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");\r
-\r
- p3.setOptionNames(new HashSet(Arrays.asList("--AAMATRIX", "--ABMAT", "--BBBB")));\r
- p3.setRequired(true);\r
- // THIS LINE IS CAUSING EXCEPTION AS DEFAULT VALUE MUST BE DEFINED\r
- // IN WITHIN POSSIBLE VALUES\r
- p3.setDefaultValue("--BBBB");\r
- p3.validate();\r
- String com = p3.toCommand("=");\r
- assertEquals("--BBBB", com);\r
- p3.setDefaultValue("--ABMAT");\r
- com = p3.toCommand("=");\r
- assertEquals("--ABMAT", com);\r
- } catch (ValidationException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- } catch (WrongParameterException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- }\r
- }\r
-\r
- @Test(expectedExceptions = IllegalStateException.class)\r
- public void testCreateNumParameterWithoutValidValue() throws MalformedURLException {\r
- try {\r
- Parameter<Mafft> p4 = new Parameter<Mafft>("Matrix", "DNA weight matrix");\r
- // This is causing exception is ValidValue constrain is not defined\r
- // for\r
- // numeric value\r
- p4.setDefaultValue("5");\r
- } catch (WrongParameterException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- }\r
-\r
- }\r
-\r
- @Test()\r
- public void testCreateParameterWithValidValueConstrain() throws MalformedURLException {\r
- Parameter<Mafft> p4 = new Parameter<Mafft>("Matrix", "DNA weight matrix");\r
- ValueConstrain vc = new ValueConstrain();\r
- vc.setType(ValueConstrain.Type.Float);\r
- vc.setMin("0");\r
- vc.setMax("10");\r
- p4.setValidValue(vc);\r
- try {\r
- p4.setDefaultValue("5");\r
- } catch (WrongParameterException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- }\r
- }\r
-\r
- @Test(expectedExceptions = WrongParameterException.class)\r
- public void testValidateLowerBoundaryConstrainCheck() throws WrongParameterException {\r
- Parameter<Mafft> p3 = new Parameter<Mafft>("Matrix1", "Protein weight matrix");\r
- // TODO publish help on a compbio web site\r
- p3.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");\r
- // This attribute is required by strict schema\r
- p3.setOptionName("--AAMATRIX");\r
- p3.setRequired(true);\r
-\r
- ValueConstrain vc = new ValueConstrain();\r
- vc.setType(ValueConstrain.Type.Float);\r
- vc.setMin("-10.12");\r
- vc.setMax("0");\r
- p3.setValidValue(vc);\r
- // THIS IS CAUSING EXCEPTION\r
- p3.setDefaultValue("-11.0");\r
- }\r
-\r
- @Test(expectedExceptions = WrongParameterException.class)\r
- public void testValidateUpperBoundaryConstrainCheck() throws WrongParameterException {\r
- Parameter<Mafft> p3 = new Parameter<Mafft>("Matrix1", "Protein weight matrix");\r
- // TODO publish help on a compbio web site\r
- p3.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");\r
- // This attribute is required by strict schema\r
- p3.setOptionName("--AAMATRIX");\r
- p3.setRequired(true);\r
-\r
- ValueConstrain vc = new ValueConstrain();\r
- vc.setType(ValueConstrain.Type.Float);\r
- vc.setMin("-10.12");\r
- vc.setMax("0");\r
- p3.setValidValue(vc);\r
- // THIS IS CAUSING EXCEPTION\r
- p3.setDefaultValue("1");\r
- }\r
-\r
- @Test()\r
- public void testValidateBoundaryConstrainCheck() {\r
- try {\r
- Parameter<Mafft> p3 = new Parameter<Mafft>("Matrix1", "Protein weight matrix");\r
- // TODO publish help on a compbio web site\r
- p3.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");\r
- // This attribute is required by strict schema\r
- p3.setOptionName("--AAMATRIX");\r
- p3.setRequired(true);\r
-\r
- ValueConstrain vc = new ValueConstrain();\r
- vc.setType(ValueConstrain.Type.Float);\r
- vc.setMin("-10.12");\r
- p3.setValidValue(vc);\r
- // Max value boundary is not defined so 1 is valid\r
- p3.setDefaultValue("1");\r
- p3.validate();\r
- } catch (WrongParameterException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- } catch (ValidationException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- }\r
- }\r
-\r
- @Test(expectedExceptions = ValidationException.class)\r
- public void testValidateValueConstrain() throws ValidationException {\r
- ValueConstrain vc = new ValueConstrain();\r
- vc.setType(ValueConstrain.Type.Float);\r
- // NO BOUNDARIES DEFINED\r
- vc.validate();\r
- }\r
-}\r
+++ /dev/null
-package compbio.stat.collector;\r
-\r
-import static org.testng.Assert.assertEquals;\r
-import static org.testng.Assert.assertFalse;\r
-import static org.testng.Assert.assertTrue;\r
-\r
-import java.io.File;\r
-import java.util.Date;\r
-import java.util.concurrent.Executors;\r
-import java.util.concurrent.ScheduledExecutorService;\r
-import java.util.concurrent.ScheduledFuture;\r
-import java.util.concurrent.TimeUnit;\r
-\r
-import org.testng.Assert;\r
-import org.testng.annotations.Test;\r
-\r
-import compbio.metadata.AllTestSuit;\r
-import compbio.stat.collector.JobDirectory;\r
-\r
-public class ExecutionStatCollectorTester {\r
-\r
- final static String LOCAL_JOBS = AllTestSuit.TEST_DATA_PATH_ABSOLUTE\r
- + "ljobs";\r
- final static String CLUSTER_JOBS = AllTestSuit.TEST_DATA_PATH_ABSOLUTE\r
- + "jobs";\r
- @Test\r
- public void testCollectStat() {\r
- ExecutionStatCollector local_jobs = new ExecutionStatCollector(\r
- LOCAL_JOBS, 1);\r
- ExecutionStatCollector cl_jobs = new ExecutionStatCollector(\r
- CLUSTER_JOBS, 24);\r
- \r
- // Collect statistics prior to call getStats()!\r
- local_jobs.collectStatistics();\r
- cl_jobs.collectStatistics();\r
- \r
- StatProcessor local_stats = local_jobs.getStats();\r
- StatProcessor cl_stats = cl_jobs.getStats();\r
- \r
- assertEquals(local_stats.getJobNumber(), 12);\r
- // ClustalW#1015343425414965 - empty\r
- assertEquals(local_stats.getIncompleteJobs().size(), 1);\r
- assertEquals(local_stats.getFailedJobs().size(), 0);\r
- assertEquals(local_stats.getAbandonedJobs().size(), 1);\r
-\r
- }\r
-\r
- @Test\r
- public void testUpdateStatTester() {\r
-\r
- ScheduledExecutorService executor = Executors.newScheduledThreadPool(1);\r
- ScheduledFuture<?> sf = executor.scheduleAtFixedRate(\r
- new ExecutionStatCollector(LOCAL_JOBS, 1), 1, 10,\r
- TimeUnit.SECONDS);\r
-\r
- try {\r
- Thread.sleep(1000 * 35);\r
- executor.shutdown();\r
- executor.awaitTermination(300, TimeUnit.SECONDS);\r
- } catch (InterruptedException e) {\r
- e.printStackTrace();\r
- Assert.fail(e.getMessage());\r
- }\r
- }\r
-\r
- /**\r
- * This test will fail in time as it relies on last access time for file in\r
- * the filesystem! This OK as it has been tested by then.\r
- * \r
- */\r
- @Test (enabled = false)\r
- public void testHasTimedOut() {\r
- ExecutionStatCollector ecol = new ExecutionStatCollector(LOCAL_JOBS, 1);\r
- File f = new File(LOCAL_JOBS + File.separator\r
- + "ClustalW#1015373448154965");\r
- File timedOut = new File(LOCAL_JOBS + File.separator\r
- + "Mafft#7868649707286965");\r
-\r
- JobDirectory jd = new JobDirectory(f);\r
- JobDirectory timedOutDir = new JobDirectory(timedOut);\r
- System.out.println("! " + new Date(f.lastModified()));\r
-\r
- assertTrue((System.currentTimeMillis() - f.lastModified())\r
- / (1000 * 60 * 60) < 1);\r
- assertFalse((System.currentTimeMillis() - timedOut.lastModified())\r
- / (1000 * 60 * 60) < 1);\r
- assertFalse(ecol.hasTimedOut(jd));\r
- assertTrue(ecol.hasTimedOut(timedOutDir));\r
- }\r
-\r
- @Test\r
- public void testHasCompleted() {\r
- ExecutionStatCollector ecol_no_timeout = new ExecutionStatCollector(\r
- LOCAL_JOBS, 10000000);\r
- ExecutionStatCollector ecol = new ExecutionStatCollector(LOCAL_JOBS, 1);\r
-\r
- File normal = new File(LOCAL_JOBS + File.separator\r
- + "ClustalW#100368900075204");\r
- File finished = new File(LOCAL_JOBS + File.separator\r
- + "ClustalW#1015373448154965");\r
- File cancelled = new File(LOCAL_JOBS + File.separator\r
- + "Mafft#7918237850044965");\r
- File noresult = new File(LOCAL_JOBS + File.separator\r
- + "ClustalW#1015343425414965");\r
-\r
- JobDirectory dnormal = new JobDirectory(normal);\r
- JobDirectory dfinished = new JobDirectory(finished);\r
- JobDirectory dcancelled = new JobDirectory(cancelled);\r
-\r
- JobDirectory dnoresult = new JobDirectory(noresult);\r
-\r
- assertTrue(ecol.hasCompleted(dnormal));\r
- assertTrue(ecol.hasCompleted(dfinished));\r
- assertTrue(ecol.hasCompleted(dcancelled));\r
-\r
- assertTrue(ecol.hasCompleted(dnoresult));\r
- assertFalse(ecol_no_timeout.hasCompleted(dnoresult));\r
-\r
- }\r
-}\r
+++ /dev/null
-package compbio.stat.collector;\r
-\r
-import static org.testng.Assert.assertEquals;\r
-import static org.testng.Assert.assertNotNull;\r
-\r
-import java.sql.SQLException;\r
-import java.sql.Timestamp;\r
-import java.util.Calendar;\r
-import java.util.Date;\r
-import java.util.List;\r
-\r
-import org.testng.Assert;\r
-import org.testng.annotations.BeforeClass;\r
-import org.testng.annotations.Test;\r
-\r
-import compbio.stat.servlet.util.StatCollection;\r
-import compbio.stat.servlet.util.Totals;\r
-import compbio.ws.client.Services;\r
-\r
-public class StatDBTester {\r
- StatDB statdb;\r
- Timestamp from;\r
- Timestamp to;\r
- \r
- @BeforeClass(alwaysRun=true )\r
- public void init() {\r
- try {\r
- statdb = new StatDB(true);\r
- Calendar fromCal = Calendar.getInstance();\r
- fromCal.set(2011, 4, 1);\r
- \r
- Calendar toCal = Calendar.getInstance();\r
- toCal.set(2011, 5, 1);\r
- from = new Timestamp(fromCal.getTimeInMillis());\r
- to = new Timestamp(toCal.getTimeInMillis());\r
- \r
- } catch (SQLException e) {\r
- e.printStackTrace();\r
- Assert.fail(e.getLocalizedMessage());\r
- }\r
- }\r
-\r
- /*\r
- * This test fails if run with other tests. This is likely due to the fact that StatDB \r
- * is initialised with connection to other then the test database from StatCollector class.\r
- * TODO look at this\r
- */\r
- @Test(enabled = false)\r
- public void testReadYearData() {\r
- Calendar cal = Calendar.getInstance();\r
- cal.set(2010, 4, 1);\r
- try {\r
- List<JobStat> jobs = statdb.readData(\r
- new Timestamp(cal.getTimeInMillis()), to, Services.MuscleWS, false);\r
- assertNotNull(jobs);\r
- assertEquals(jobs.size(), 1294);\r
- // statdb.shutdownDBServer();\r
- } catch (SQLException e) {\r
- e.printStackTrace();\r
- Assert.fail(e.getMessage());\r
- }\r
-\r
- }\r
-\r
- /*\r
- * This test fails if run with other tests. This is likely due to the fact that StatDB \r
- * is initialised with connection to other then the test database from StatCollector class.\r
- * TODO look at this\r
- */\r
- @Test(enabled =false)\r
- public void testReadOneMonthData() {\r
- try {\r
- List<JobStat> jobs = statdb.readData(from, to, Services.TcoffeeWS, false);\r
- assertNotNull(jobs);\r
- assertEquals(jobs.size(), 36);\r
-\r
- jobs = statdb.readData(from,to, Services.ClustalWS,false);\r
-\r
- assertNotNull(jobs);\r
- assertEquals(jobs.size(), 137);\r
-\r
- jobs = statdb.readData(from, to, Services.MafftWS,false);\r
- assertNotNull(jobs);\r
- assertEquals(jobs.size(), 136);\r
-\r
- jobs = statdb.readData(from,to, Services.ProbconsWS,false);\r
- assertNotNull(jobs);\r
- assertEquals(jobs.size(), 9);\r
-\r
- jobs = statdb.readData(from,to, Services.MuscleWS,false);\r
- assertNotNull(jobs);\r
- assertEquals(jobs.size(), 63);\r
-\r
- } catch (SQLException e) {\r
- e.printStackTrace();\r
- Assert.fail(e.getMessage());\r
- }\r
- }\r
-\r
- /*\r
- * This test fails if run with other tests. This is likely due to the fact that StatDB \r
- * is initialised with connection to other then the test database from StatCollector class.\r
- * TODO look at this\r
- */\r
- @Test(enabled=false)\r
- public void testGetEarliestRecord() {\r
- try {\r
- Date earliestRec = statdb.getEarliestRecord();\r
- \r
- assertEquals(1278543600000L, earliestRec.getTime());\r
- } catch (SQLException e) {\r
- e.printStackTrace();\r
- Assert.fail(e.getLocalizedMessage());\r
- }\r
-\r
- }\r
-\r
- @Test(sequential=true)\r
- public void testVerifyJobsCount() {\r
-\r
- try {\r
- Calendar cal = Calendar.getInstance();\r
- cal.add(Calendar.MONTH, -5);\r
- Timestamp from = new Timestamp(cal.getTimeInMillis());\r
- cal.add(Calendar.MONTH, 1);\r
- Timestamp to = new Timestamp(cal.getTimeInMillis());\r
- StatCollection sc = StatCollection.newStatCollecton(from, to);\r
- Totals t = Totals.sumStats(sc.getAllStat());\r
-\r
- //System.out.println(sc.getAllStat());\r
- \r
- assertEquals(t.getTotal(), statdb.getTotalJobsCount(from, to));\r
- assertEquals(t.getAbandoned(), statdb.getAbandonedCount(from, to));\r
- assertEquals(t.getCancelled(), statdb.getCancelledCount(from, to));\r
- assertEquals(t.getIncomplete(), statdb.getIncompleteCount(from, to));\r
-\r
- } catch (SQLException e) {\r
- e.printStackTrace();\r
- Assert.fail(e.getLocalizedMessage());\r
- }\r
-\r
- }\r
-}\r
+++ /dev/null
-package compbio.stat.collector;\r
-\r
-import java.io.File;\r
-import java.io.IOException;\r
-\r
-import org.testng.Assert;\r
-import org.testng.annotations.Test;\r
-\r
-import compbio.metadata.AllTestSuit;\r
-\r
-public class TestInputFilter {\r
-\r
- final static String FASTA_INPUT = AllTestSuit.TEST_DATA_PATH_ABSOLUTE\r
- + "TO1381.fasta";\r
- final static String ALN_INPUT = AllTestSuit.TEST_DATA_PATH_ABSOLUTE\r
- + "TO1381L.aln";\r
- final static String TEST_FASTA_INPUT = AllTestSuit.TEST_DATA_PATH_ABSOLUTE\r
- + "test_input.fasta";\r
- final static String TEST_ALIGNMENT_INPUT = AllTestSuit.TEST_DATA_PATH_ABSOLUTE\r
- + "test_input.aln";\r
- @Test\r
- public void TestInputFilter() {\r
- InputFilter ifilter = new InputFilter();\r
- try {\r
- // Makes sure real files are accepted\r
- Assert.assertTrue(ifilter.accept(new File(FASTA_INPUT)));\r
- Assert.assertTrue(ifilter.accept(new File(ALN_INPUT)));\r
-\r
- // .. and test files are not\r
- Assert.assertFalse(ifilter.accept(new File(TEST_ALIGNMENT_INPUT)));\r
- Assert.assertFalse(ifilter.accept(new File(TEST_FASTA_INPUT)));\r
- // does not matter if the file is empty, it is still not a test\r
- // file!\r
- Assert.assertTrue(ifilter.accept(File.createTempFile("aaa", "bbb")));\r
- } catch (IOException e) {\r
- e.printStackTrace();\r
- Assert.fail(e.getMessage());\r
- }\r
- }\r
-}\r
+++ /dev/null
-package compbio.stat.servlet.util;\r
-\r
-import java.sql.SQLException;\r
-import java.util.Calendar;\r
-import java.util.Date;\r
-import java.util.GregorianCalendar;\r
-import java.util.Map;\r
-\r
-import org.testng.Assert;\r
-import org.testng.annotations.Test;\r
-\r
-public class StatCollectionTester {\r
-\r
- @Test\r
- public void testGetStats() {\r
- Map<Date, Totals> stats;\r
- Calendar cal = GregorianCalendar.getInstance();\r
- cal.add(Calendar.MONTH, -3);\r
-\r
- try {\r
- stats = StatCollection.getStats(cal.getTime());\r
-\r
- } catch (SQLException e) {\r
- e.printStackTrace();\r
- Assert.fail(e.getMessage());\r
- }\r
-\r
- }\r
-\r
-}\r
+++ /dev/null
-package compbio.ws.client;\r
-\r
-import java.io.ByteArrayInputStream;\r
-import java.io.FileNotFoundException;\r
-import java.io.IOException;\r
-import java.io.PrintWriter;\r
-import java.io.Writer;\r
-import java.util.List;\r
-\r
-import compbio.data.msa.SequenceAnnotation;\r
-import compbio.data.sequence.FastaSequence;\r
-import compbio.data.sequence.ScoreManager;\r
-import compbio.data.sequence.SequenceUtil;\r
-import compbio.metadata.JobSubmissionException;\r
-import compbio.metadata.Preset;\r
-import compbio.metadata.PresetManager;\r
-import compbio.metadata.ResultNotAvailableException;\r
-import compbio.metadata.UnsupportedRuntimeException;\r
-import compbio.metadata.WrongParameterException;\r
-import compbio.runner.conservation.AACon;\r
-\r
-/**\r
- * AAConWS client example\r
- */\r
-public class AAConWSClientExample {\r
-\r
- /*\r
- * Input sequences. For the simplicity keep them in the class\r
- */\r
- static final String input = ">Foo \r\n"\r
- + "MTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV\r\n"\r
- + "ARLGRVRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQL\r\n"\r
- + "LPEEPYITAQLLNWRRRLCDWRALDVLSAQVRAAVAQGVGAVEPFAFLSEDASAAEQLAC\r\n"\r
- + "ARTRAQAIAASVRPLAPTRVRSKGPLRVGFVSNGFGAHPTGLLTVALFEALQRRQPDLQM\r\n"\r
- + "HLFATSGDDGSTLRTRLAQASTLHDVTALGHLATAKHIRHHGIDLLFDLRGWGGGGRPEV\r\n"\r
- + "FALRPAPVQVNWLAYPGTSGAPWMDYVLGDAFALPPALEPFYSEHVLRLQGAFQPSDTSR\r\n"\r
- + "VVAEPPSRTQCGLPEQGVVLCCFNNSYKLNPQSMARMLAVLREVPDSVLWLLSGPGEADA\r\n"\r
- + "RLRAFAHAQGVDAQRLVFMPKLPHPQYLARYRHADLFLDTHPYNAHTTASDALWTGCPVL\r\n"\r
- + "TTPGETFAARVAGSLNHHLGLDEMNVADDAAFVAKAVALASDPAALTALHARVDVLRRES\r\n"\r
- + "GVFEMDGFADDFGALLQALARRHGWLGI\r\n"\r
- + "\r\n"\r
- + ">Bar \r\n"\r
- + "-----------------------------------MGDTTAGEMAVQRGLALH-------\r\n"\r
- + "---------QQRHAEAAVLLQQASDAAPEHPGIALWL-HALEDAGQAEAAAA-YTRAHQL\r\n"\r
- + "LPEEPYITAQLLN--------------------AVAQGVGAVEPFAFLSEDASAAE----\r\n"\r
- + "----------SVRPLAPTRVRSKGPLRVGFVSNGFGAHPTGLLTVALFEALQRRQPDLQM\r\n"\r
- + "HLFATSGDDGSTLRTRLAQASTLHDVTALGHLATAKHIRHHGIDLLFDLRGWGGGGRPEV\r\n"\r
- + "FALRPAPVQVNWLAYPGTSGAPWMDYVLGDAFALPPALEPFYSEHVLRLQGAFQPSDTSR\r\n"\r
- + "VVAEPPSRTQCGLPEQGVVLCCFNNSYKLNPQSMARMLAVLREVPDSVLWLLSGPGEADA\r\n"\r
- + "RLRAFAHAQGVDAQRLVFMPKLPHPQYLARYRHADLFLDTHPYNAHTTASDALWTGCPVL\r\n"\r
- + "TTPGETFAARVAGSLNHHLGLDEMNVADDAAFVAKAVALASDPAALTALHARVDVLRRES\r\n"\r
- + "GVFEMDGFADDFGALLQALARRHGWLGI\r\n"\r
- + "\r\n"\r
- + ">Noname \r\n"\r
- + "-MTADGPRELLQLRAAVRHRPQDVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV\r\n"\r
- + "ARLGRVRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALED--------------HQL\r\n"\r
- + "LPEEPYITAQLDVLSAQVR-------------AAVAQGVGAVEPFAFLSEDASAAEQLAC\r\n"\r
- + "ARTRAQAIAASVRPLAPTRVRSKGPLRVGFVSNGFGAHPTGLLTVALFEALQRRQPDLQM\r\n"\r
- + "HLFATSGDDGSTLRTRLAQASTLHDVTALGHLATAKHIRHHGIDLLFDLRGWGGGGRPEV\r\n"\r
- + "FALRPAPVQVNWLAYPGTSGAPWMDYVLGDAFALPPALEPFYSEHVLRLQGAFQPSDTSR\r\n"\r
- + "VVAEPPSRTQCGLPEQGVVLCCFNNSYKLNPQSMARMLAVLREVPDSVLWLLSGPGEADA\r\n"\r
- + "RLRAFAHAQGVDAQRLVFMPKLPHPQYLARYRHADLFLDTHPYNAHTTASDALWTGCPVL\r\n"\r
- + "TTPGETFAARVAGSLNHHLGLDEMNVADDAAFVAKAVALASDPAALTALHARVDVLRRES\r\n"\r
- + "I---------------------------";\r
-\r
- public static void main(String[] args) throws UnsupportedRuntimeException,\r
- JobSubmissionException, WrongParameterException,\r
- FileNotFoundException, IOException, ResultNotAvailableException,\r
- InterruptedException {\r
-\r
- /*\r
- * Annotation interface for AAConWS web service instance\r
- */\r
- SequenceAnnotation<AACon> client = (SequenceAnnotation<AACon>) Jws2Client\r
- .connect("http://www.compbio.dundee.ac.uk/aacon",\r
- Services.AAConWS);\r
-\r
- /* Get the list of available presets */\r
- PresetManager presetman = client.getPresets();\r
-\r
- /* Get the Preset object by preset name */\r
- Preset preset = presetman.getPresetByName("Complete conservation");\r
-\r
- /*\r
- * Load sequences in FASTA format from the file You can use something\r
- * like new FileInputStream() to load sequence from the file\r
- */\r
- List<FastaSequence> fastalist = SequenceUtil\r
- .readFasta(new ByteArrayInputStream(input.getBytes()));\r
-\r
- /*\r
- * Submit loaded sequences for an alignment using preset. The job\r
- * identifier is returned by this method, you can retrieve the results\r
- * with it sometime later.\r
- */\r
- String jobId = client.presetAnalize(fastalist, preset);\r
-\r
- /* This method will block for the duration of the calculation */\r
- ScoreManager result = client.getAnnotation(jobId);\r
-\r
- /*\r
- * This is a better way of obtaining results, it does not involve\r
- * holding the connection open for the duration of the calculation,\r
- * Besides, as the University of Dundee public server will reset the\r
- * connection after 10 minutes of idling, this is the only way to obtain\r
- * the results of long running task from our public server.\r
- */\r
- // while (client.getJobStatus(jobId) != JobStatus.FINISHED) {\r
- // Thread.sleep(1000); // wait a second, then recheck the status\r
- // }\r
-\r
- /* Output the alignment to standard out */\r
- Writer writer = new PrintWriter(System.out, true);\r
- IOHelper.writeOut(writer, result);\r
- writer.close();\r
- // Score.write(result, System.out);\r
-\r
- /* Alternatively, you can record retrieved alignment into the file */\r
- // FileOutputStream out = new FileOutputStream("result.txt");\r
- // Score.write(result, out);\r
- // out.close();\r
- }\r
-}\r
+++ /dev/null
-package compbio.ws.client;\r
-\r
-import static org.testng.Assert.assertEquals;\r
-import static org.testng.Assert.assertNotNull;\r
-import static org.testng.Assert.fail;\r
-import static org.testng.Assert.assertTrue;\r
-import java.io.File;\r
-import java.io.FileInputStream;\r
-import java.io.FileNotFoundException;\r
-import java.io.IOException;\r
-import java.net.ConnectException;\r
-import java.util.ArrayList;\r
-import java.util.List;\r
-\r
-import javax.xml.ws.WebServiceException;\r
-\r
-import org.testng.annotations.BeforeTest;\r
-import org.testng.annotations.Test;\r
-\r
-import compbio.data.msa.JABAService;\r
-import compbio.data.msa.SequenceAnnotation;\r
-import compbio.data.sequence.ConservationMethod;\r
-import compbio.data.sequence.FastaSequence;\r
-import compbio.data.sequence.ScoreManager;\r
-import compbio.data.sequence.SequenceUtil;\r
-import compbio.metadata.AllTestSuit;\r
-import compbio.metadata.JobSubmissionException;\r
-import compbio.metadata.LimitExceededException;\r
-import compbio.metadata.Option;\r
-import compbio.metadata.Preset;\r
-import compbio.metadata.PresetManager;\r
-import compbio.metadata.ResultNotAvailableException;\r
-import compbio.metadata.RunnerConfig;\r
-import compbio.metadata.UnsupportedRuntimeException;\r
-import compbio.metadata.WrongParameterException;\r
-import compbio.runner.conservation.AACon;\r
-import compbio.util.SysPrefs;\r
-\r
-public class TestAAConWS {\r
-\r
- SequenceAnnotation<AACon> msaws;\r
-\r
- @BeforeTest(groups = {AllTestSuit.test_group_webservices})\r
- void initConnection() {\r
- /*\r
- * URL url = null; try { url = new\r
- * URL("http://localhost:8080/jabaws/AAConWS?wsdl"); } catch\r
- * (MalformedURLException e) { e.printStackTrace();\r
- * fail(e.getLocalizedMessage()); } String namespace =\r
- * "http://msa.data.compbio/01/12/2010/"; QName qname = new\r
- * QName(namespace, "AAConWS"); Service serv = Service.create(url,\r
- * qname); msaws = serv.getPort(new QName(namespace, "AAConWSPort"),\r
- * Annotation.class);\r
- */try {\r
- JABAService client = Jws2Client.connect(\r
- "http://localhost:8080/jabaws", Services.AAConWS);\r
- msaws = (SequenceAnnotation<AACon>) client;\r
- } catch (ConnectException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- } catch (WebServiceException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- }\r
- }\r
-\r
- @Test(groups = {AllTestSuit.test_group_webservices})\r
- public void testAnalize() throws FileNotFoundException, IOException {\r
-\r
- /*\r
- * MsaWS msaws = serv.getPort(new QName(\r
- * "http://msa.data.compbio/01/01/2010/", "ClustalWSPort"),\r
- * MsaWS.class);\r
- */\r
- // Annotation<AACon> msaws = serv.getPort(new QName(namespace,\r
- // "ClustalWSPort"), Annotation.class);\r
-\r
- // List<FastaSequence> fsl = SequenceUtil.readFasta(new FileInputStream(\r
- // AAConTester.test_alignment_input));\r
-\r
- String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory()\r
- + File.separator;\r
-\r
- List<FastaSequence> fsl = SequenceUtil.readFasta(new FileInputStream(\r
- CURRENT_DIRECTORY + "testsrc" + File.separator + "testdata"\r
- + File.separator + "TO1381.fasta.aln"));\r
-\r
- try {\r
- System.out.println("Pres: " + msaws.getPresets().getPresets());\r
- String jobId = msaws.analize(fsl);\r
- System.out.println("J: " + jobId);\r
- ScoreManager result = msaws.getAnnotation(jobId);\r
- assertNotNull(result);\r
- assertEquals(result.asSet().size(), 1);\r
-\r
- assertEquals(result.asSet().iterator().next().getMethod(),\r
- ConservationMethod.SHENKIN.toString());\r
- List<Float> scores = result.asSet().iterator().next().getScores();\r
- assertNotNull(scores);\r
- assertEquals(scores.size(), 568);\r
-\r
- // Using presets\r
- PresetManager<AACon> presets = msaws.getPresets();\r
- jobId = msaws.presetAnalize(fsl,\r
- presets.getPresetByName("Quick conservation"));\r
- result = msaws.getAnnotation(jobId);\r
- assertNotNull(result);\r
- assertEquals(result.asSet().size(), 13);\r
-\r
- jobId = msaws.presetAnalize(fsl,\r
- presets.getPresetByName("Slow conservation"));\r
- result = msaws.getAnnotation(jobId);\r
- assertNotNull(result);\r
- assertEquals(result.asSet().size(), 5);\r
-\r
- jobId = msaws.presetAnalize(fsl,\r
- presets.getPresetByName("Complete conservation"));\r
- result = msaws.getAnnotation(jobId);\r
- assertNotNull(result);\r
- assertEquals(result.asSet().size(), 18);\r
-\r
- } catch (UnsupportedRuntimeException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- } catch (LimitExceededException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- } catch (JobSubmissionException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- } catch (ResultNotAvailableException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- } catch (WrongParameterException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- }\r
-\r
- }\r
- @Test(groups = {AllTestSuit.test_group_webservices})\r
- public void testRecoverArgsForPreset() throws Exception {\r
- PresetManager<AACon> presets = msaws.getPresets();\r
- for (Preset<AACon> preset:presets.getPresets())\r
- {\r
- List<Option<AACon>> args = preset.getArguments(msaws.getRunnerOptions());\r
- List opts = preset.getOptions();\r
- assertTrue(args.size()>=opts.size(),"Couldn't recover all Option items for preset "+preset.getName());\r
- }\r
- }\r
- @Test(groups = {AllTestSuit.test_group_webservices})\r
- public void testPresetAnalize() throws FileNotFoundException, IOException {\r
-\r
- String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory()\r
- + File.separator;\r
-\r
- List<FastaSequence> fsl = SequenceUtil.readFasta(new FileInputStream(\r
- CURRENT_DIRECTORY + "testsrc" + File.separator + "testdata"\r
- + File.separator + "TO1381.fasta.aln"));\r
-\r
- try {\r
- System.out.println("Pres: " + msaws.getPresets().getPresets());\r
-\r
- // Using presets\r
- PresetManager<AACon> presets = msaws.getPresets();\r
- String jobId = msaws.presetAnalize(fsl,\r
- presets.getPresetByName("Quick conservation"));\r
- ScoreManager result = msaws.getAnnotation(jobId);\r
- assertNotNull(result);\r
- assertEquals(result.asSet().size(), 13);\r
-\r
- jobId = msaws.presetAnalize(fsl,\r
- presets.getPresetByName("Slow conservation"));\r
- result = msaws.getAnnotation(jobId);\r
- assertNotNull(result);\r
- assertEquals(result.asSet().size(), 5);\r
-\r
- jobId = msaws.presetAnalize(fsl,\r
- presets.getPresetByName("Complete conservation"));\r
- result = msaws.getAnnotation(jobId);\r
- assertNotNull(result);\r
- assertEquals(result.asSet().size(), 18);\r
-\r
- } catch (UnsupportedRuntimeException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- } catch (LimitExceededException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- } catch (JobSubmissionException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- } catch (ResultNotAvailableException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- } catch (WrongParameterException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- }\r
-\r
- }\r
-\r
- @Test(groups = {AllTestSuit.test_group_webservices})\r
- public void testCustomAnalize() throws FileNotFoundException, IOException {\r
-\r
- String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory()\r
- + File.separator;\r
-\r
- List<FastaSequence> fsl = SequenceUtil.readFasta(new FileInputStream(\r
- CURRENT_DIRECTORY + "testsrc" + File.separator + "testdata"\r
- + File.separator + "TO1381.fasta.aln"));\r
-\r
- // Using options\r
- RunnerConfig<AACon> options = msaws.getRunnerOptions();\r
- // System.out.println(options.getArguments());\r
-\r
- try {\r
- List<Option<AACon>> args = new ArrayList<Option<AACon>>();\r
- Option<AACon> arg,normarg;\r
- args.add(arg=options.getArgument("SMERFS"));\r
- args.add(normarg=options.getArgument("Normalize"));\r
- arg.setValue(arg.getPossibleValues().get(0));\r
- // options.getArgument("SMERFS Column Scoring Method")\r
- // .setDefaultValue("MAX_SCORE");\r
- // options.getArgument("SMERFS Gap Threshhold").setDefaultValue("1");\r
- String jobId = msaws.customAnalize(fsl, args);\r
- ScoreManager result = msaws.getAnnotation(jobId);\r
- assertNotNull(result);\r
- assertEquals(result.asSet().size(), 1);\r
- assertEquals(result.asSet().iterator().next().getScores().get(0),\r
- 0.698f);\r
- args.remove(normarg); // remove normalization argument\r
- // System.out.println(options);\r
- jobId = msaws.customAnalize(fsl, args);\r
- result = msaws.getAnnotation(jobId);\r
- assertNotNull(result);\r
- assertEquals(result.asSet().size(), 1);\r
- assertEquals(result.asSet().iterator().next().getScores().get(0),\r
- 0.401f);\r
-\r
- } catch (WrongParameterException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- } catch (UnsupportedRuntimeException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- } catch (LimitExceededException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- } catch (JobSubmissionException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- } catch (ResultNotAvailableException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- }\r
- }\r
-}\r
+++ /dev/null
-package compbio.ws.client;
-
-import static org.testng.Assert.assertEquals;
-import static org.testng.Assert.assertNotNull;
-import static org.testng.Assert.fail;
-
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.net.ConnectException;
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.xml.ws.WebServiceException;
-
-import org.testng.annotations.BeforeTest;
-import org.testng.annotations.Test;
-
-import compbio.data.msa.JABAService;
-import compbio.data.msa.SequenceAnnotation;
-import compbio.data.sequence.ConservationMethod;
-import compbio.data.sequence.FastaSequence;
-import compbio.data.sequence.ScoreManager;
-import compbio.data.sequence.SequenceUtil;
-import compbio.metadata.AllTestSuit;
-import compbio.metadata.JobSubmissionException;
-import compbio.metadata.LimitExceededException;
-import compbio.metadata.Option;
-import compbio.metadata.PresetManager;
-import compbio.metadata.ResultNotAvailableException;
-import compbio.metadata.RunnerConfig;
-import compbio.metadata.UnsupportedRuntimeException;
-import compbio.metadata.WrongParameterException;
-import compbio.runner.conservation.AACon;
-import compbio.util.SysPrefs;
-import compbio.ws.server.IUPredWS;
-
-public class TestIUPredWS {
-
- SequenceAnnotation<IUPredWS> msaws;
-
- @BeforeTest(groups = {AllTestSuit.test_group_webservices})
- void initConnection() {
- /*
- * URL url = null; try { url = new
- * URL("http://localhost:8080/jabaws/AAConWS?wsdl"); } catch
- * (MalformedURLException e) { e.printStackTrace();
- * fail(e.getLocalizedMessage()); } String namespace =
- * "http://msa.data.compbio/01/12/2010/"; QName qname = new
- * QName(namespace, "AAConWS"); Service serv = Service.create(url,
- * qname); msaws = serv.getPort(new QName(namespace, "AAConWSPort"),
- * Annotation.class);
- */try {
- JABAService client = Jws2Client.connect(
- "http://localhost:8080/jabaws", Services.IUPredWS);
- msaws = (SequenceAnnotation<IUPredWS>) client;
- } catch (ConnectException e) {
- e.printStackTrace();
- fail(e.getMessage());
- } catch (WebServiceException e) {
- e.printStackTrace();
- fail(e.getMessage());
- }
- }
-
- @Test(groups = {AllTestSuit.test_group_webservices})
- public void testCustomAnalize() throws FileNotFoundException, IOException {
-
- String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory()
- + File.separator;
-
- List<FastaSequence> fsl = SequenceUtil.readFasta(new FileInputStream(
- CURRENT_DIRECTORY + "testsrc" + File.separator + "testdata"
- + File.separator + "TO1381.fasta"));
-
- try {
- List<Option<IUPredWS>> opts=new ArrayList<Option<IUPredWS>>();
- opts.add(msaws.getRunnerOptions().getArgumentByOptionName("Long"));
- String jobId = msaws.customAnalize(fsl,opts);
- System.out.println("J: " + jobId);
- ScoreManager result = msaws.getAnnotation(jobId);
- assertNotNull(result);
-// assertEquals(result.asSet().size(), 1);
-
- } catch (UnsupportedRuntimeException e) {
- e.printStackTrace();
- fail(e.getMessage());
- } catch (LimitExceededException e) {
- e.printStackTrace();
- fail(e.getMessage());
- } catch (JobSubmissionException e) {
- e.printStackTrace();
- fail(e.getMessage());
- } catch (ResultNotAvailableException e) {
- e.printStackTrace();
- fail(e.getMessage());
- } catch (WrongParameterException e) {
- e.printStackTrace();
- fail(e.getMessage());
- }
-
- }
-}
+++ /dev/null
- package compbio.ws.client;
-
-import static org.testng.Assert.assertNotNull;
-import static org.testng.Assert.fail;
-
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.io.OutputStreamWriter;
-import java.io.Writer;
-import java.net.ConnectException;
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.xml.ws.WebServiceException;
-
-import org.testng.annotations.BeforeTest;
-import org.testng.annotations.Test;
-
-import compbio.data.msa.JABAService;
-import compbio.data.msa.SequenceAnnotation;
-import compbio.data.sequence.Alignment;
-import compbio.data.sequence.ClustalAlignmentUtil;
-import compbio.data.sequence.FastaSequence;
-import compbio.data.sequence.RNAStructScoreManager;
-import compbio.data.sequence.UnknownFileFormatException;
-import compbio.metadata.AllTestSuit;
-import compbio.metadata.JobSubmissionException;
-import compbio.metadata.LimitExceededException;
-import compbio.metadata.Option;
-import compbio.metadata.ResultNotAvailableException;
-import compbio.metadata.UnsupportedRuntimeException;
-import compbio.metadata.WrongParameterException;
-import compbio.ws.server.RNAalifoldWS;
-
-
-public class TestRNAalifoldWS {
-
- SequenceAnnotation<RNAalifoldWS> foldws;
-// RNAalifoldWS foldws;
-
- @BeforeTest(groups = {AllTestSuit.test_group_webservices})
- void initConnection() {
-
- try {
- JABAService client = Jws2Client.connect(
- "http://localhost:8080/jabaws", Services.RNAalifoldWS);
-// foldws = (RNAalifoldWS) client;
- foldws = (SequenceAnnotation<RNAalifoldWS>) client;
- } catch (ConnectException e) {
- e.printStackTrace();
- fail(e.getMessage());
- } catch (WebServiceException e) {
- e.printStackTrace();
- fail(e.getMessage());
- }
- }
-
-
- @Test(groups = {AllTestSuit.test_group_webservices})
- public void testFold() throws FileNotFoundException, IOException,
- UnknownFileFormatException {
-
- Alignment aln = ClustalAlignmentUtil.readClustalFile(new FileInputStream(
- AllTestSuit.test_input_aln));
-
- List<FastaSequence> fsl = aln.getSequences();
-
- try {
- List<Option<RNAalifoldWS>> options = new ArrayList<Option<RNAalifoldWS>>();
- options.add(foldws.getRunnerOptions().getArgumentByOptionName("--mis"));
- options.add(foldws.getRunnerOptions().getArgumentByOptionName("-p"));
- options.add(foldws.getRunnerOptions().getArgumentByOptionName("--MEA"));
-
- System.out.println("TestRNAalifoldWS: print options: " + options.toString());
-
- String jobId = foldws.customAnalize(fsl, options);
- System.out.println("J: " + jobId);
- RNAStructScoreManager result = (RNAStructScoreManager)foldws.getAnnotation(jobId);
-
- Writer writer = new OutputStreamWriter(System.out);
- result.writeOut(writer);
-
- assertNotNull(result);
-
- } catch (UnsupportedRuntimeException e) {
- e.printStackTrace();
- fail(e.getMessage());
- } catch (LimitExceededException e) {
- e.printStackTrace();
- fail(e.getMessage());
- } catch (JobSubmissionException e) {
- e.printStackTrace();
- fail(e.getMessage());
- } catch (ResultNotAvailableException e) {
- e.printStackTrace();
- fail(e.getMessage());
- } catch (WrongParameterException e) {
- e.printStackTrace();
- fail(e.getMessage());
- }
- }
-}
-
-
-
+++ /dev/null
-package compbio.ws.client;\r
-\r
-import static org.testng.Assert.assertTrue;\r
-import static org.testng.Assert.fail;\r
-\r
-import java.io.PrintWriter;\r
-import java.net.ConnectException;\r
-import javax.xml.ws.WebServiceException;\r
-import org.testng.annotations.Test;\r
-import compbio.metadata.AllTestSuit;\r
-\r
-public class WSTesterTester {\r
-\r
- public static final String SERVER = "http://localhost:8080/jabaws";\r
- // public static final String SERVER = "http://192.168.202.130/jabaws";\r
-\r
- // public static final String SERVER =\r
- // "http://nanna.cluster.lifesci.dundee.ac.uk:8080/jaba";\r
-\r
- @Test(groups = {AllTestSuit.test_group_webservices})\r
- public void testAllWindowsWS() {\r
- WSTester tester = new WSTester(SERVER,\r
- new PrintWriter(System.out, true));\r
- try {\r
- assertTrue(tester.checkService(Services.AAConWS));\r
- assertTrue(tester.checkService(Services.JronnWS));\r
- assertTrue(tester.checkService(Services.ClustalWS));\r
- assertTrue(tester.checkService(Services.MuscleWS));\r
- assertTrue(tester.checkService(Services.ClustalOWS));\r
- assertTrue(tester.checkService(Services.IUPredWS));\r
- } catch (ConnectException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- } catch (WebServiceException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- }\r
-\r
- // Will throw UnsupportedRuntimeException on windows\r
- // ws = Jws2Client.connect(SERVER, Services.MafftWS);\r
- // assertTrue(tester.checkService(ws));\r
-\r
- }\r
-\r
- @Test(groups = {AllTestSuit.test_group_webservices})\r
- public void testAllWS() {\r
- WSTester tester = new WSTester(SERVER, new PrintWriter(System.out));\r
- try {\r
- for (Services service : Services.values()) {\r
- assertTrue(tester.checkService(service));\r
- }\r
- } catch (ConnectException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- } catch (WebServiceException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- }\r
- }\r
-\r
-}\r
+++ /dev/null
-package compbio.ws.server;\r
-\r
-import static org.testng.Assert.assertNotNull;\r
-import static org.testng.Assert.assertTrue;\r
-import static org.testng.Assert.fail;\r
-\r
-import java.io.File;\r
-import java.io.FileInputStream;\r
-import java.io.FileNotFoundException;\r
-import java.io.IOException;\r
-import java.net.ConnectException;\r
-import java.util.Arrays;\r
-import java.util.List;\r
-import java.util.Set;\r
-\r
-import javax.xml.ws.WebServiceException;\r
-\r
-import org.testng.annotations.Test;\r
-\r
-import compbio.data.msa.MsaWS;\r
-import compbio.data.sequence.FastaSequence;\r
-import compbio.data.sequence.SequenceUtil;\r
-import compbio.metadata.AllTestSuit;\r
-import compbio.metadata.ChunkHolder;\r
-import compbio.metadata.JobStatus;\r
-import compbio.metadata.JobSubmissionException;\r
-import compbio.metadata.ResultNotAvailableException;\r
-import compbio.ws.client.Jws2Client;\r
-import compbio.ws.client.Services;\r
-import compbio.ws.client.WSTesterTester;\r
-\r
-public class RegistryWSTester {\r
-\r
- @Test(groups = {AllTestSuit.test_group_webservices,\r
- AllTestSuit.test_group_windows_only})\r
- public void testGetSupportedServices() {\r
- try {\r
- compbio.data.msa.RegistryWS reg = Jws2Client\r
- .connectToRegistry(WSTesterTester.SERVER);\r
- System.out.println(reg.getSupportedServices());\r
- Set<Services> supserv = reg.getSupportedServices();\r
- assertTrue(supserv.containsAll(Arrays.asList(new Services[]{\r
- Services.AAConWS, Services.ClustalOWS, Services.IUPredWS,\r
- Services.MuscleWS, Services.ClustalWS, Services.JronnWS})));\r
- } catch (ConnectException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (WebServiceException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- }\r
- }\r
- @Test(groups = {AllTestSuit.test_group_webservices})\r
- public void testTestService() {\r
- compbio.data.msa.RegistryWS reg = null;\r
- try {\r
- reg = Jws2Client.connectToRegistry(WSTesterTester.SERVER);\r
- assertNotNull(reg.testService(Services.AAConWS));\r
- } catch (ConnectException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (WebServiceException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- }\r
- }\r
-\r
- @Test(dependsOnMethods = {"testTestService"}, groups = {AllTestSuit.test_group_webservices})\r
- public void testIsOperating() {\r
- try {\r
- compbio.data.msa.RegistryWS reg = Jws2Client\r
- .connectToRegistry(WSTesterTester.SERVER);\r
- assertTrue(reg.isOperating(Services.AAConWS));\r
- } catch (ConnectException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (WebServiceException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- }\r
- }\r
-\r
- @Test(dependsOnMethods = {"testTestService"}, groups = {AllTestSuit.test_group_webservices})\r
- public void testGetLastTestedOn() {\r
- try {\r
- compbio.data.msa.RegistryWS reg = Jws2Client\r
- .connectToRegistry(WSTesterTester.SERVER);\r
- assertNotNull(reg.getLastTestedOn(Services.AAConWS));\r
- } catch (ConnectException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (WebServiceException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- }\r
- }\r
-\r
- @Test(dependsOnMethods = {"testTestService"}, groups = {AllTestSuit.test_group_webservices})\r
- public void testGetLastTested() {\r
- try {\r
- Thread.sleep(1000);\r
- } catch (InterruptedException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- }\r
- try {\r
- compbio.data.msa.RegistryWS reg = Jws2Client\r
- .connectToRegistry(WSTesterTester.SERVER);\r
- System.out.println(reg.getLastTested(Services.AAConWS));\r
- assertTrue(reg.getLastTested(Services.AAConWS) > 0);\r
- } catch (ConnectException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (WebServiceException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- }\r
- }\r
-\r
- @Test(groups = {AllTestSuit.test_group_webservices})\r
- public void testTestAllServices() {\r
- try {\r
- compbio.data.msa.RegistryWS reg = Jws2Client\r
- .connectToRegistry(WSTesterTester.SERVER);\r
- System.out.println(reg.testAllServices());\r
- } catch (ConnectException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (WebServiceException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- }\r
- }\r
-\r
- @Test(groups = {AllTestSuit.test_group_webservices})\r
- public void testProgressReporting() {\r
- MsaWS service = null;\r
- try {\r
- service = (MsaWS) Jws2Client.connect(\r
- "http://www.compbio.dundee.ac.uk/jabaws",\r
- // "http://webserv1.cluster.lifesci.dundee.ac.uk:8089/jabaws",\r
- Services.ProbconsWS);\r
- File input = new File(AllTestSuit.TEST_DATA_PATH_ABSOLUTE\r
- + "200x500Protein.fasta");\r
- assertTrue(input.exists());\r
- List<FastaSequence> fs = SequenceUtil\r
- .readFasta(new FileInputStream(input));\r
- String jobId = service.align(fs);\r
- Thread.sleep(5000);\r
- ChunkHolder pos = null;\r
- while (service.getJobStatus(jobId) == JobStatus.RUNNING) {\r
- if (pos == null) {\r
- pos = service.pullExecStatistics(jobId, 0);\r
- } else {\r
- pos = service.pullExecStatistics(jobId,\r
- pos.getNextPosition());\r
- }\r
- Thread.sleep(10);\r
- System.out.print(pos.getChunk());\r
- }\r
- System.out.println();\r
- System.out.println(service.getResult(jobId));\r
- } catch (ConnectException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (WebServiceException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (ResultNotAvailableException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (FileNotFoundException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (IOException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (JobSubmissionException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (InterruptedException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- }\r
- }\r
-\r
- @Test(groups = {AllTestSuit.test_group_webservices})\r
- public void testPullRunningJob() {\r
- MsaWS service = null;\r
- try {\r
- service = (MsaWS) Jws2Client.connect(\r
- "http://webserv1.cluster.lifesci.dundee.ac.uk:8089/jabaws",\r
- Services.ProbconsWS);\r
- String jobId = "@Probcons#158079030012566";\r
- ChunkHolder pos = null;\r
- while (service.getJobStatus(jobId) == JobStatus.RUNNING) {\r
- if (pos == null) {\r
- pos = service.pullExecStatistics(jobId, 0);\r
- } else {\r
- pos = service.pullExecStatistics(jobId,\r
- pos.getNextPosition());\r
- }\r
- Thread.sleep(10);\r
- System.out.print(pos.getChunk());\r
- }\r
- System.out.println();\r
- System.out.println(service.getResult(jobId));\r
- } catch (ConnectException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (WebServiceException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (ResultNotAvailableException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (InterruptedException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- }\r
- }\r
-}\r
git://source.jalview.org / proteocache.git / commitdiff